diff --git a/internal/api/handler/agent_groups.go b/internal/api/handler/agent_groups.go
index 6eef3a6..e97cda9 100644
--- a/internal/api/handler/agent_groups.go
+++ b/internal/api/handler/agent_groups.go
@@ -1,6 +1,7 @@
 package handler
 
 import (
+	"context"
 	"encoding/json"
 	"net/http"
 	"strconv"
@@ -12,12 +13,12 @@ import (
 
 // AgentGroupService defines the service interface for agent group operations.
 type AgentGroupService interface {
-	ListAgentGroups(page, perPage int) ([]domain.AgentGroup, int64, error)
-	GetAgentGroup(id string) (*domain.AgentGroup, error)
-	CreateAgentGroup(group domain.AgentGroup) (*domain.AgentGroup, error)
-	UpdateAgentGroup(id string, group domain.AgentGroup) (*domain.AgentGroup, error)
-	DeleteAgentGroup(id string) error
-	ListMembers(id string) ([]domain.Agent, int64, error)
+	ListAgentGroups(ctx context.Context, page, perPage int) ([]domain.AgentGroup, int64, error)
+	GetAgentGroup(ctx context.Context, id string) (*domain.AgentGroup, error)
+	CreateAgentGroup(ctx context.Context, group domain.AgentGroup) (*domain.AgentGroup, error)
+	UpdateAgentGroup(ctx context.Context, id string, group domain.AgentGroup) (*domain.AgentGroup, error)
+	DeleteAgentGroup(ctx context.Context, id string) error
+	ListMembers(ctx context.Context, id string) ([]domain.Agent, int64, error)
 }
 
 // AgentGroupHandler handles HTTP requests for agent group operations.
@@ -54,7 +55,7 @@ func (h AgentGroupHandler) ListAgentGroups(w http.ResponseWriter, r *http.Reques
 		}
 	}
 
-	groups, total, err := h.svc.ListAgentGroups(page, perPage)
+	groups, total, err := h.svc.ListAgentGroups(r.Context(), page, perPage)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to list agent groups", requestID)
 		return
@@ -86,7 +87,7 @@ func (h AgentGroupHandler) GetAgentGroup(w http.ResponseWriter, r *http.Request)
 		return
 	}
 
-	group, err := h.svc.GetAgentGroup(id)
+	group, err := h.svc.GetAgentGroup(r.Context(), id)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusNotFound, "Agent group not found", requestID)
 		return
@@ -120,7 +121,7 @@ func (h AgentGroupHandler) CreateAgentGroup(w http.ResponseWriter, r *http.Reque
 		return
 	}
 
-	created, err := h.svc.CreateAgentGroup(group)
+	created, err := h.svc.CreateAgentGroup(r.Context(), group)
 	if err != nil {
 		if strings.Contains(err.Error(), "invalid") || strings.Contains(err.Error(), "required") {
 			ErrorWithRequestID(w, http.StatusBadRequest, err.Error(), requestID)
@@ -157,7 +158,7 @@ func (h AgentGroupHandler) UpdateAgentGroup(w http.ResponseWriter, r *http.Reque
 		return
 	}
 
-	updated, err := h.svc.UpdateAgentGroup(id, group)
+	updated, err := h.svc.UpdateAgentGroup(r.Context(), id, group)
 	if err != nil {
 		if strings.Contains(err.Error(), "not found") {
 			ErrorWithRequestID(w, http.StatusNotFound, "Agent group not found", requestID)
@@ -186,7 +187,7 @@ func (h AgentGroupHandler) DeleteAgentGroup(w http.ResponseWriter, r *http.Reque
 		return
 	}
 
-	if err := h.svc.DeleteAgentGroup(id); err != nil {
+	if err := h.svc.DeleteAgentGroup(r.Context(), id); err != nil {
 		if strings.Contains(err.Error(), "not found") {
 			ErrorWithRequestID(w, http.StatusNotFound, "Agent group not found", requestID)
 			return
@@ -217,7 +218,7 @@ func (h AgentGroupHandler) ListAgentGroupMembers(w http.ResponseWriter, r *http.
 	}
 	id := parts[0]
 
-	members, total, err := h.svc.ListMembers(id)
+	members, total, err := h.svc.ListMembers(r.Context(), id)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to list group members", requestID)
 		return
diff --git a/internal/api/handler/agents.go b/internal/api/handler/agents.go
index 85ad542..2e5b42e 100644
--- a/internal/api/handler/agents.go
+++ b/internal/api/handler/agents.go
@@ -1,6 +1,7 @@
 package handler
 
 import (
+	"context"
 	"encoding/json"
 	"net/http"
 	"strconv"
@@ -12,16 +13,16 @@ import (
 
 // AgentService defines the service interface for agent operations.
 type AgentService interface {
-	ListAgents(page, perPage int) ([]domain.Agent, int64, error)
-	GetAgent(id string) (*domain.Agent, error)
-	RegisterAgent(agent domain.Agent) (*domain.Agent, error)
-	Heartbeat(agentID string, metadata *domain.AgentMetadata) error
-	CSRSubmit(agentID string, csrPEM string) (string, error)
-	CSRSubmitForCert(agentID string, certID string, csrPEM string) (string, error)
-	CertificatePickup(agentID, certID string) (string, error)
-	GetWork(agentID string) ([]domain.Job, error)
-	GetWorkWithTargets(agentID string) ([]domain.WorkItem, error)
-	UpdateJobStatus(agentID string, jobID string, status string, errMsg string) error
+	ListAgents(ctx context.Context, page, perPage int) ([]domain.Agent, int64, error)
+	GetAgent(ctx context.Context, id string) (*domain.Agent, error)
+	RegisterAgent(ctx context.Context, agent domain.Agent) (*domain.Agent, error)
+	Heartbeat(ctx context.Context, agentID string, metadata *domain.AgentMetadata) error
+	CSRSubmit(ctx context.Context, agentID string, csrPEM string) (string, error)
+	CSRSubmitForCert(ctx context.Context, agentID string, certID string, csrPEM string) (string, error)
+	CertificatePickup(ctx context.Context, agentID, certID string) (string, error)
+	GetWork(ctx context.Context, agentID string) ([]domain.Job, error)
+	GetWorkWithTargets(ctx context.Context, agentID string) ([]domain.WorkItem, error)
+	UpdateJobStatus(ctx context.Context, agentID string, jobID string, status string, errMsg string) error
 }
 
 // AgentHandler handles HTTP requests for agent operations.
@@ -58,7 +59,7 @@ func (h AgentHandler) ListAgents(w http.ResponseWriter, r *http.Request) {
 		}
 	}
 
-	agents, total, err := h.svc.ListAgents(page, perPage)
+	agents, total, err := h.svc.ListAgents(r.Context(), page, perPage)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to list agents", requestID)
 		return
@@ -92,7 +93,7 @@ func (h AgentHandler) GetAgent(w http.ResponseWriter, r *http.Request) {
 	}
 	id = parts[0]
 
-	agent, err := h.svc.GetAgent(id)
+	agent, err := h.svc.GetAgent(r.Context(), id)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusNotFound, "Agent not found", requestID)
 		return
@@ -131,7 +132,7 @@ func (h AgentHandler) RegisterAgent(w http.ResponseWriter, r *http.Request) {
 		return
 	}
 
-	created, err := h.svc.RegisterAgent(agent)
+	created, err := h.svc.RegisterAgent(r.Context(), agent)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to register agent", requestID)
 		return
@@ -182,7 +183,7 @@ func (h AgentHandler) Heartbeat(w http.ResponseWriter, r *http.Request) {
 		}
 	}
 
-	if err := h.svc.Heartbeat(agentID, metadata); err != nil {
+	if err := h.svc.Heartbeat(r.Context(), agentID, metadata); err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to record heartbeat", requestID)
 		return
 	}
@@ -234,9 +235,9 @@ func (h AgentHandler) AgentCSRSubmit(w http.ResponseWriter, r *http.Request) {
 
 	// If certificate_id is provided, sign the CSR for that specific certificate
 	if req.CertificateID != "" {
-		status, err = h.svc.CSRSubmitForCert(agentID, req.CertificateID, req.CSRPEM)
+		status, err = h.svc.CSRSubmitForCert(r.Context(), agentID, req.CertificateID, req.CSRPEM)
 	} else {
-		status, err = h.svc.CSRSubmit(agentID, req.CSRPEM)
+		status, err = h.svc.CSRSubmit(r.Context(), agentID, req.CSRPEM)
 	}
 
 	if err != nil {
@@ -271,7 +272,7 @@ func (h AgentHandler) AgentCertificatePickup(w http.ResponseWriter, r *http.Requ
 	agentID := parts[0]
 	certID := parts[2]
 
-	certPEM, err := h.svc.CertificatePickup(agentID, certID)
+	certPEM, err := h.svc.CertificatePickup(r.Context(), agentID, certID)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusNotFound, "Certificate not found or not ready", requestID)
 		return
@@ -303,7 +304,7 @@ func (h AgentHandler) AgentGetWork(w http.ResponseWriter, r *http.Request) {
 	}
 	agentID := parts[0]
 
-	workItems, err := h.svc.GetWorkWithTargets(agentID)
+	workItems, err := h.svc.GetWorkWithTargets(r.Context(), agentID)
 	if err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to get pending work", requestID)
 		return
@@ -353,7 +354,7 @@ func (h AgentHandler) AgentReportJobStatus(w http.ResponseWriter, r *http.Reques
 		return
 	}
 
-	if err := h.svc.UpdateJobStatus(agentID, jobID, req.Status, req.Error); err != nil {
+	if err := h.svc.UpdateJobStatus(r.Context(), agentID, jobID, req.Status, req.Error); err != nil {
 		ErrorWithRequestID(w, http.StatusInternalServerError, "Failed to update job status", requestID)
 		return
 	}
diff --git a/internal/connector/issuer/acme/dns.go b/internal/connector/issuer/acme/dns.go
index 1b1cd44..92cb9a3 100644
--- a/internal/connector/issuer/acme/dns.go
+++ b/internal/connector/issuer/acme/dns.go
@@ -6,6 +6,8 @@ import (
 	"log/slog"
 	"os/exec"
 	"time"
+
+	"github.com/shankar0123/certctl/internal/validation"
 )
 
 // DNSSolver defines the interface for DNS-01 challenge provisioning.
@@ -55,6 +57,16 @@ func (s *ScriptDNSSolver) Present(ctx context.Context, domain, token, keyAuth st
 		return fmt.Errorf("DNS present script not configured")
 	}
 
+	// Validate domain name to prevent injection attacks
+	if err := validation.ValidateDomainName(domain); err != nil {
+		return fmt.Errorf("invalid domain name: %w", err)
+	}
+
+	// Validate ACME token to prevent injection attacks
+	if err := validation.ValidateACMEToken(token); err != nil {
+		return fmt.Errorf("invalid ACME token: %w", err)
+	}
+
 	fqdn := "_acme-challenge." + domain
 
 	s.Logger.Info("creating DNS TXT record via script",
@@ -72,6 +84,16 @@ func (s *ScriptDNSSolver) CleanUp(ctx context.Context, domain, token, keyAuth st
 		return nil
 	}
 
+	// Validate domain name to prevent injection attacks
+	if err := validation.ValidateDomainName(domain); err != nil {
+		return fmt.Errorf("invalid domain name: %w", err)
+	}
+
+	// Validate ACME token to prevent injection attacks
+	if err := validation.ValidateACMEToken(token); err != nil {
+		return fmt.Errorf("invalid ACME token: %w", err)
+	}
+
 	fqdn := "_acme-challenge." + domain
 
 	s.Logger.Info("removing DNS TXT record via script",
@@ -90,6 +112,16 @@ func (s *ScriptDNSSolver) PresentPersist(ctx context.Context, domain, token, rec
 		return fmt.Errorf("DNS present script not configured")
 	}
 
+	// Validate domain name to prevent injection attacks
+	if err := validation.ValidateDomainName(domain); err != nil {
+		return fmt.Errorf("invalid domain name: %w", err)
+	}
+
+	// Validate ACME token to prevent injection attacks
+	if err := validation.ValidateACMEToken(token); err != nil {
+		return fmt.Errorf("invalid ACME token: %w", err)
+	}
+
 	fqdn := "_validation-persist." + domain
 
 	s.Logger.Info("creating persistent DNS TXT record via script",
diff --git a/internal/connector/issuer/acme/dns_test.go b/internal/connector/issuer/acme/dns_test.go
index d11c051..e99119d 100644
--- a/internal/connector/issuer/acme/dns_test.go
+++ b/internal/connector/issuer/acme/dns_test.go
@@ -193,3 +193,136 @@ echo "FQDN=$CERTCTL_DNS_FQDN" > ` + outputFile + `
 		}
 	})
 }
+
+// Security tests for DNS injection prevention
+
+func TestScriptDNSSolver_Present_RejectInvalidDomain(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	scriptPath := filepath.Join(tmpDir, "present.sh")
+	os.WriteFile(scriptPath, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	tests := []struct {
+		name   string
+		domain string
+	}{
+		{
+			name:   "domain with command injection semicolon",
+			domain: "example.com; rm -rf /",
+		},
+		{
+			name:   "domain with backtick injection",
+			domain: "example.com`whoami`",
+		},
+		{
+			name:   "domain with command substitution",
+			domain: "example.com$(whoami)",
+		},
+		{
+			name:   "domain with pipe injection",
+			domain: "example.com | cat /etc/passwd",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			solver := acmeissuer.NewScriptDNSSolver(scriptPath, "", logger)
+			err := solver.Present(ctx, tt.domain, "test-token", "test-key-auth")
+			if err == nil {
+				t.Fatalf("expected error for invalid domain: %s", tt.domain)
+			}
+		})
+	}
+}
+
+func TestScriptDNSSolver_Present_RejectInvalidToken(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	scriptPath := filepath.Join(tmpDir, "present.sh")
+	os.WriteFile(scriptPath, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	tests := []struct {
+		name  string
+		token string
+	}{
+		{
+			name:  "token with command injection",
+			token: "token$(whoami)",
+		},
+		{
+			name:  "token with backtick injection",
+			token: "token`id`",
+		},
+		{
+			name:  "token with semicolon",
+			token: "token;malicious",
+		},
+		{
+			name:  "token with pipe",
+			token: "token|cat",
+		},
+		{
+			name:  "token with space",
+			token: "token value",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			solver := acmeissuer.NewScriptDNSSolver(scriptPath, "", logger)
+			err := solver.Present(ctx, "example.com", tt.token, "test-key-auth")
+			if err == nil {
+				t.Fatalf("expected error for invalid token: %s", tt.token)
+			}
+		})
+	}
+}
+
+func TestScriptDNSSolver_CleanUp_RejectInvalidDomain(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	scriptPath := filepath.Join(tmpDir, "cleanup.sh")
+	os.WriteFile(scriptPath, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	solver := acmeissuer.NewScriptDNSSolver("", scriptPath, logger)
+	err := solver.CleanUp(ctx, "example.com; rm -rf /", "test-token", "test-key-auth")
+	if err == nil {
+		t.Fatal("expected error for command injection in domain")
+	}
+}
+
+func TestScriptDNSSolver_PresentPersist_RejectInvalidDomain(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	scriptPath := filepath.Join(tmpDir, "present.sh")
+	os.WriteFile(scriptPath, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	solver := acmeissuer.NewScriptDNSSolver(scriptPath, "", logger)
+	err := solver.PresentPersist(ctx, "example.com`whoami`", "test-token", "letsencrypt.org; accounturi=https://example.com/acct/1")
+	if err == nil {
+		t.Fatal("expected error for command injection in domain")
+	}
+}
+
+func TestScriptDNSSolver_PresentPersist_RejectInvalidToken(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	scriptPath := filepath.Join(tmpDir, "present.sh")
+	os.WriteFile(scriptPath, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	solver := acmeissuer.NewScriptDNSSolver(scriptPath, "", logger)
+	err := solver.PresentPersist(ctx, "example.com", "token$(whoami)", "letsencrypt.org; accounturi=https://example.com/acct/1")
+	if err == nil {
+		t.Fatal("expected error for command injection in token")
+	}
+}
diff --git a/internal/connector/issuer/openssl/openssl.go b/internal/connector/issuer/openssl/openssl.go
index e97f203..2388d41 100644
--- a/internal/connector/issuer/openssl/openssl.go
+++ b/internal/connector/issuer/openssl/openssl.go
@@ -97,22 +97,28 @@ func (c *Connector) ValidateConfig(ctx context.Context, rawConfig json.RawMessag
 		return fmt.Errorf("sign_script is required")
 	}
 
-	// Verify sign_script exists and is executable
-	if _, err := os.Stat(cfg.SignScript); err != nil {
+	// Verify sign_script exists and is a regular file
+	if info, err := os.Stat(cfg.SignScript); err != nil {
 		return fmt.Errorf("sign_script not accessible: %w", err)
+	} else if !info.Mode().IsRegular() {
+		return fmt.Errorf("sign_script must be a regular file, got %s", info.Mode())
 	}
 
-	// Verify revoke_script exists if specified
+	// Verify revoke_script exists and is a regular file if specified
 	if cfg.RevokeScript != "" {
-		if _, err := os.Stat(cfg.RevokeScript); err != nil {
+		if info, err := os.Stat(cfg.RevokeScript); err != nil {
 			return fmt.Errorf("revoke_script not accessible: %w", err)
+		} else if !info.Mode().IsRegular() {
+			return fmt.Errorf("revoke_script must be a regular file, got %s", info.Mode())
 		}
 	}
 
-	// Verify crl_script exists if specified
+	// Verify crl_script exists and is a regular file if specified
 	if cfg.CRLScript != "" {
-		if _, err := os.Stat(cfg.CRLScript); err != nil {
+		if info, err := os.Stat(cfg.CRLScript); err != nil {
 			return fmt.Errorf("crl_script not accessible: %w", err)
+		} else if !info.Mode().IsRegular() {
+			return fmt.Errorf("crl_script must be a regular file, got %s", info.Mode())
 		}
 	}
 
diff --git a/internal/connector/issuer/openssl/openssl_test.go b/internal/connector/issuer/openssl/openssl_test.go
index 955caca..3d8ded8 100644
--- a/internal/connector/issuer/openssl/openssl_test.go
+++ b/internal/connector/issuer/openssl/openssl_test.go
@@ -556,3 +556,68 @@ func generateMockCertPEM() string {
 		Bytes: certBytes,
 	}))
 }
+
+// Security tests for script path validation
+
+func TestOpenSSLConnector_ValidateConfig_RejectNonRegularFile(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	// Try to use a directory as a script path
+	tmpDir := t.TempDir()
+
+	config := &openssl.Config{
+		SignScript: tmpDir, // This is a directory, not a regular file
+	}
+	connector := openssl.New(config, logger)
+
+	rawConfig, _ := json.Marshal(config)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("Expected error when sign_script is not a regular file")
+	}
+}
+
+func TestOpenSSLConnector_ValidateConfig_ValidateRevokeScriptPath(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	signScript := filepath.Join(tmpDir, "sign.sh")
+	os.WriteFile(signScript, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	// Try to use a nonexistent file as revoke_script
+	config := &openssl.Config{
+		SignScript:   signScript,
+		RevokeScript: "/nonexistent/revoke.sh",
+	}
+	connector := openssl.New(config, logger)
+
+	rawConfig, _ := json.Marshal(config)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("Expected error when revoke_script is nonexistent")
+	}
+}
+
+func TestOpenSSLConnector_ValidateConfig_ValidateCRLScriptPath(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	signScript := filepath.Join(tmpDir, "sign.sh")
+	os.WriteFile(signScript, []byte("#!/bin/sh\nexit 0"), 0755)
+
+	// Try to use a directory as crl_script
+	config := &openssl.Config{
+		SignScript: signScript,
+		CRLScript:  tmpDir, // This is a directory, not a regular file
+	}
+	connector := openssl.New(config, logger)
+
+	rawConfig, _ := json.Marshal(config)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("Expected error when crl_script is not a regular file")
+	}
+}
diff --git a/internal/connector/target/apache/apache.go b/internal/connector/target/apache/apache.go
index 6def055..52ab74f 100644
--- a/internal/connector/target/apache/apache.go
+++ b/internal/connector/target/apache/apache.go
@@ -142,7 +142,7 @@ func (c *Connector) DeployCertificate(ctx context.Context, request target.Deploy
 
 	// Validate Apache configuration before reload
 	c.logger.Debug("validating Apache configuration", "validate_command", c.config.ValidateCommand)
-	validateCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ValidateCommand)
+	validateCmd := exec.CommandContext(ctx, c.config.ValidateCommand)
 	if output, err := validateCmd.CombinedOutput(); err != nil {
 		errMsg := fmt.Sprintf("Apache config validation failed: %v (output: %s)", err, string(output))
 		c.logger.Error("Apache validation failed", "error", err, "output", string(output))
@@ -156,7 +156,7 @@ func (c *Connector) DeployCertificate(ctx context.Context, request target.Deploy
 
 	// Graceful reload
 	c.logger.Debug("reloading Apache", "reload_command", c.config.ReloadCommand)
-	reloadCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ReloadCommand)
+	reloadCmd := exec.CommandContext(ctx, c.config.ReloadCommand)
 	if output, err := reloadCmd.CombinedOutput(); err != nil {
 		errMsg := fmt.Sprintf("Apache reload failed: %v (output: %s)", err, string(output))
 		c.logger.Error("Apache reload failed", "error", err, "output", string(output))
@@ -196,7 +196,7 @@ func (c *Connector) ValidateDeployment(ctx context.Context, request target.Valid
 	startTime := time.Now()
 
 	// Validate Apache configuration
-	validateCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ValidateCommand)
+	validateCmd := exec.CommandContext(ctx, c.config.ValidateCommand)
 	if output, err := validateCmd.CombinedOutput(); err != nil {
 		errMsg := fmt.Sprintf("Apache config validation failed: %v (output: %s)", err, string(output))
 		c.logger.Error("validation failed", "error", err)
diff --git a/internal/connector/target/haproxy/haproxy.go b/internal/connector/target/haproxy/haproxy.go
index 2d4dba2..85ce13a 100644
--- a/internal/connector/target/haproxy/haproxy.go
+++ b/internal/connector/target/haproxy/haproxy.go
@@ -10,6 +10,7 @@ import (
 	"time"
 
 	"github.com/shankar0123/certctl/internal/connector/target"
+	"github.com/shankar0123/certctl/internal/validation"
 )
 
 // Config represents the HAProxy deployment target configuration.
@@ -53,12 +54,22 @@ func (c *Connector) ValidateConfig(ctx context.Context, rawConfig json.RawMessag
 		return fmt.Errorf("HAProxy reload_command is required")
 	}
 
+	// Validate commands to prevent injection attacks
+	if err := validation.ValidateShellCommand(cfg.ReloadCommand); err != nil {
+		return fmt.Errorf("invalid reload_command: %w", err)
+	}
+	if cfg.ValidateCommand != "" {
+		if err := validation.ValidateShellCommand(cfg.ValidateCommand); err != nil {
+			return fmt.Errorf("invalid validate_command: %w", err)
+		}
+	}
+
 	c.logger.Info("validating HAProxy configuration",
 		"pem_path", cfg.PEMPath)
 
 	// Verify validate command works if provided
 	if cfg.ValidateCommand != "" {
-		cmd := exec.CommandContext(ctx, "sh", "-c", cfg.ValidateCommand)
+		cmd := exec.CommandContext(ctx, cfg.ValidateCommand)
 		if err := cmd.Run(); err != nil {
 			c.logger.Warn("HAProxy config validation failed during config check",
 				"error", err,
@@ -114,7 +125,7 @@ func (c *Connector) DeployCertificate(ctx context.Context, request target.Deploy
 	// Validate HAProxy configuration if validate command is configured
 	if c.config.ValidateCommand != "" {
 		c.logger.Debug("validating HAProxy configuration", "validate_command", c.config.ValidateCommand)
-		validateCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ValidateCommand)
+		validateCmd := exec.CommandContext(ctx, c.config.ValidateCommand)
 		if output, err := validateCmd.CombinedOutput(); err != nil {
 			errMsg := fmt.Sprintf("HAProxy config validation failed: %v (output: %s)", err, string(output))
 			c.logger.Error("HAProxy validation failed", "error", err, "output", string(output))
@@ -129,7 +140,7 @@ func (c *Connector) DeployCertificate(ctx context.Context, request target.Deploy
 
 	// Reload HAProxy
 	c.logger.Debug("reloading HAProxy", "reload_command", c.config.ReloadCommand)
-	reloadCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ReloadCommand)
+	reloadCmd := exec.CommandContext(ctx, c.config.ReloadCommand)
 	if output, err := reloadCmd.CombinedOutput(); err != nil {
 		errMsg := fmt.Sprintf("HAProxy reload failed: %v (output: %s)", err, string(output))
 		c.logger.Error("HAProxy reload failed", "error", err, "output", string(output))
@@ -169,7 +180,7 @@ func (c *Connector) ValidateDeployment(ctx context.Context, request target.Valid
 
 	// Validate HAProxy configuration if command provided
 	if c.config.ValidateCommand != "" {
-		validateCmd := exec.CommandContext(ctx, "sh", "-c", c.config.ValidateCommand)
+		validateCmd := exec.CommandContext(ctx, c.config.ValidateCommand)
 		if output, err := validateCmd.CombinedOutput(); err != nil {
 			errMsg := fmt.Sprintf("HAProxy config validation failed: %v (output: %s)", err, string(output))
 			c.logger.Error("validation failed", "error", err)
diff --git a/internal/connector/target/nginx/nginx_test.go b/internal/connector/target/nginx/nginx_test.go
index dd1dd76..f76f7ef 100644
--- a/internal/connector/target/nginx/nginx_test.go
+++ b/internal/connector/target/nginx/nginx_test.go
@@ -377,3 +377,85 @@ func TestNginxConnector_ValidateDeployment_ValidateCommandFails(t *testing.T) {
 		t.Fatal("expected invalid result")
 	}
 }
+
+// Security tests for command injection prevention
+
+func TestNginxConnector_ValidateConfig_RejectCommandInjectionSemicolon(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	cfg := nginx.Config{
+		CertPath:        filepath.Join(tmpDir, "cert.pem"),
+		ChainPath:       filepath.Join(tmpDir, "chain.pem"),
+		ReloadCommand:   "nginx; rm -rf /", // Command injection attempt
+		ValidateCommand: "true",
+	}
+
+	connector := nginx.New(&cfg, logger)
+	rawConfig, _ := json.Marshal(cfg)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("expected error for command injection in reload_command")
+	}
+}
+
+func TestNginxConnector_ValidateConfig_RejectCommandInjectionPipe(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	cfg := nginx.Config{
+		CertPath:        filepath.Join(tmpDir, "cert.pem"),
+		ChainPath:       filepath.Join(tmpDir, "chain.pem"),
+		ReloadCommand:   "true",
+		ValidateCommand: "nginx -t | cat /etc/passwd", // Command injection attempt
+	}
+
+	connector := nginx.New(&cfg, logger)
+	rawConfig, _ := json.Marshal(cfg)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("expected error for command injection in validate_command")
+	}
+}
+
+func TestNginxConnector_ValidateConfig_RejectCommandSubstitution(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	cfg := nginx.Config{
+		CertPath:        filepath.Join(tmpDir, "cert.pem"),
+		ChainPath:       filepath.Join(tmpDir, "chain.pem"),
+		ReloadCommand:   "echo $(whoami)",
+		ValidateCommand: "true",
+	}
+
+	connector := nginx.New(&cfg, logger)
+	rawConfig, _ := json.Marshal(cfg)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("expected error for command substitution in reload_command")
+	}
+}
+
+func TestNginxConnector_ValidateConfig_RejectBackticks(t *testing.T) {
+	logger := slog.New(slog.NewTextHandler(os.Stdout, &slog.HandlerOptions{Level: slog.LevelDebug}))
+	ctx := context.Background()
+
+	tmpDir := t.TempDir()
+	cfg := nginx.Config{
+		CertPath:        filepath.Join(tmpDir, "cert.pem"),
+		ChainPath:       filepath.Join(tmpDir, "chain.pem"),
+		ReloadCommand:   "true",
+		ValidateCommand: "nginx -t `whoami`",
+	}
+
+	connector := nginx.New(&cfg, logger)
+	rawConfig, _ := json.Marshal(cfg)
+	err := connector.ValidateConfig(ctx, rawConfig)
+	if err == nil {
+		t.Fatal("expected error for backtick injection in validate_command")
+	}
+}
diff --git a/internal/service/agent.go b/internal/service/agent.go
index 93628f4..285937c 100644
--- a/internal/service/agent.go
+++ b/internal/service/agent.go
@@ -105,8 +105,9 @@ func (s *AgentService) HeartbeatWithContext(ctx context.Context, agentID string,
 }
 
 // Heartbeat updates agent heartbeat (handler interface method).
-func (s *AgentService) Heartbeat(agentID string, metadata *domain.AgentMetadata) error {
-	return s.HeartbeatWithContext(context.Background(), agentID, metadata)
+// Note: This method is called from handlers which have a context; callers should prefer HeartbeatWithContext.
+func (s *AgentService) Heartbeat(ctx context.Context, agentID string, metadata *domain.AgentMetadata) error {
+	return s.HeartbeatWithContext(ctx, agentID, metadata)
 }
 
 // SubmitCSR validates and processes a Certificate Signing Request from an agent.
@@ -326,7 +327,7 @@ func (s *AgentService) GetAgentByAPIKey(ctx context.Context, apiKey string) (*do
 }
 
 // ListAgents returns paginated agents (handler interface method).
-func (s *AgentService) ListAgents(page, perPage int) ([]domain.Agent, int64, error) {
+func (s *AgentService) ListAgents(ctx context.Context, page, perPage int) ([]domain.Agent, int64, error) {
 	if page < 1 {
 		page = 1
 	}
@@ -334,7 +335,7 @@ func (s *AgentService) ListAgents(page, perPage int) ([]domain.Agent, int64, err
 		perPage = 50
 	}
 
-	agents, err := s.agentRepo.List(context.Background())
+	agents, err := s.agentRepo.List(ctx)
 	if err != nil {
 		return nil, 0, fmt.Errorf("failed to list agents: %w", err)
 	}
@@ -360,12 +361,12 @@ func (s *AgentService) ListAgents(page, perPage int) ([]domain.Agent, int64, err
 }
 
 // GetAgent returns a single agent (handler interface method).
-func (s *AgentService) GetAgent(id string) (*domain.Agent, error) {
-	return s.agentRepo.Get(context.Background(), id)
+func (s *AgentService) GetAgent(ctx context.Context, id string) (*domain.Agent, error) {
+	return s.agentRepo.Get(ctx, id)
 }
 
 // RegisterAgent creates and registers a new agent (handler interface method).
-func (s *AgentService) RegisterAgent(agent domain.Agent) (*domain.Agent, error) {
+func (s *AgentService) RegisterAgent(ctx context.Context, agent domain.Agent) (*domain.Agent, error) {
 	agent.ID = generateID("agent")
 	apiKey := generateAPIKey()
 	agent.APIKeyHash = hashAPIKey(apiKey)
@@ -374,7 +375,7 @@ func (s *AgentService) RegisterAgent(agent domain.Agent) (*domain.Agent, error)
 	agent.RegisteredAt = now
 	agent.LastHeartbeatAt = &now
 
-	if err := s.agentRepo.Create(context.Background(), &agent); err != nil {
+	if err := s.agentRepo.Create(ctx, &agent); err != nil {
 		return nil, fmt.Errorf("failed to register agent: %w", err)
 	}
 	return &agent, nil
@@ -382,8 +383,8 @@ func (s *AgentService) RegisterAgent(agent domain.Agent) (*domain.Agent, error)
 
 // CSRSubmit processes a CSR submission from an agent (handler interface method).
 // The csrPEM parameter contains "certID:csrPEM" or just the CSR PEM.
-func (s *AgentService) CSRSubmit(agentID string, csrPEM string) (string, error) {
-	err := s.SubmitCSR(context.Background(), agentID, "", []byte(csrPEM))
+func (s *AgentService) CSRSubmit(ctx context.Context, agentID string, csrPEM string) (string, error) {
+	err := s.SubmitCSR(ctx, agentID, "", []byte(csrPEM))
 	if err != nil {
 		return "", err
 	}
@@ -391,8 +392,8 @@ func (s *AgentService) CSRSubmit(agentID string, csrPEM string) (string, error)
 }
 
 // CSRSubmitForCert processes a CSR submission for a specific certificate (handler interface method).
-func (s *AgentService) CSRSubmitForCert(agentID string, certID string, csrPEM string) (string, error) {
-	err := s.SubmitCSR(context.Background(), agentID, certID, []byte(csrPEM))
+func (s *AgentService) CSRSubmitForCert(ctx context.Context, agentID string, certID string, csrPEM string) (string, error) {
+	err := s.SubmitCSR(ctx, agentID, certID, []byte(csrPEM))
 	if err != nil {
 		return "", err
 	}
@@ -400,8 +401,8 @@ func (s *AgentService) CSRSubmitForCert(agentID string, certID string, csrPEM st
 }
 
 // GetWork returns pending deployment jobs for an agent (handler interface method).
-func (s *AgentService) GetWork(agentID string) ([]domain.Job, error) {
-	jobs, err := s.GetPendingWork(context.Background(), agentID)
+func (s *AgentService) GetWork(ctx context.Context, agentID string) ([]domain.Job, error) {
+	jobs, err := s.GetPendingWork(ctx, agentID)
 	if err != nil {
 		return nil, err
 	}
@@ -417,8 +418,8 @@ func (s *AgentService) GetWork(agentID string) ([]domain.Job, error) {
 // GetWorkWithTargets returns actionable jobs enriched with target/certificate details.
 // Deployment jobs include target type + config. AwaitingCSR jobs include common name + SANs
 // so the agent knows what CSR to generate.
-func (s *AgentService) GetWorkWithTargets(agentID string) ([]domain.WorkItem, error) {
-	jobs, err := s.GetPendingWork(context.Background(), agentID)
+func (s *AgentService) GetWorkWithTargets(ctx context.Context, agentID string) ([]domain.WorkItem, error) {
+	jobs, err := s.GetPendingWork(ctx, agentID)
 	if err != nil {
 		return nil, err
 	}
@@ -438,7 +439,7 @@ func (s *AgentService) GetWorkWithTargets(agentID string) ([]domain.WorkItem, er
 
 		// Enrich with target details for deployment jobs
 		if j.TargetID != nil && *j.TargetID != "" {
-			target, err := s.targetRepo.Get(context.Background(), *j.TargetID)
+			target, err := s.targetRepo.Get(ctx, *j.TargetID)
 			if err == nil && target != nil {
 				item.TargetType = string(target.Type)
 				item.TargetConfig = target.Config
@@ -447,7 +448,7 @@ func (s *AgentService) GetWorkWithTargets(agentID string) ([]domain.WorkItem, er
 
 		// Enrich with certificate details for AwaitingCSR jobs (agent needs CN + SANs for CSR)
 		if j.Status == domain.JobStatusAwaitingCSR {
-			cert, err := s.certRepo.Get(context.Background(), j.CertificateID)
+			cert, err := s.certRepo.Get(ctx, j.CertificateID)
 			if err == nil && cert != nil {
 				item.CommonName = cert.CommonName
 				item.SANs = cert.SANs
@@ -461,13 +462,13 @@ func (s *AgentService) GetWorkWithTargets(agentID string) ([]domain.WorkItem, er
 }
 
 // UpdateJobStatus reports a job's status from an agent (handler interface method).
-func (s *AgentService) UpdateJobStatus(agentID string, jobID string, status string, errMsg string) error {
-	return s.ReportJobStatus(context.Background(), agentID, jobID, domain.JobStatus(status), errMsg)
+func (s *AgentService) UpdateJobStatus(ctx context.Context, agentID string, jobID string, status string, errMsg string) error {
+	return s.ReportJobStatus(ctx, agentID, jobID, domain.JobStatus(status), errMsg)
 }
 
 // CertificatePickup retrieves a certificate for an agent (handler interface method).
-func (s *AgentService) CertificatePickup(agentID, certID string) (string, error) {
-	certPEM, err := s.GetCertificateForAgent(context.Background(), agentID, certID)
+func (s *AgentService) CertificatePickup(ctx context.Context, agentID, certID string) (string, error) {
+	certPEM, err := s.GetCertificateForAgent(ctx, agentID, certID)
 	if err != nil {
 		return "", err
 	}
diff --git a/internal/service/agent_group.go b/internal/service/agent_group.go
index 41932a6..5e9f148 100644
--- a/internal/service/agent_group.go
+++ b/internal/service/agent_group.go
@@ -28,7 +28,7 @@ func NewAgentGroupService(
 }
 
 // ListAgentGroups returns paginated agent groups (handler interface method).
-func (s *AgentGroupService) ListAgentGroups(page, perPage int) ([]domain.AgentGroup, int64, error) {
+func (s *AgentGroupService) ListAgentGroups(ctx context.Context, page, perPage int) ([]domain.AgentGroup, int64, error) {
 	if page < 1 {
 		page = 1
 	}
@@ -36,7 +36,7 @@ func (s *AgentGroupService) ListAgentGroups(page, perPage int) ([]domain.AgentGr
 		perPage = 50
 	}
 
-	groups, err := s.groupRepo.List(context.Background())
+	groups, err := s.groupRepo.List(ctx)
 	if err != nil {
 		return nil, 0, fmt.Errorf("failed to list agent groups: %w", err)
 	}
@@ -53,12 +53,12 @@ func (s *AgentGroupService) ListAgentGroups(page, perPage int) ([]domain.AgentGr
 }
 
 // GetAgentGroup returns a single agent group (handler interface method).
-func (s *AgentGroupService) GetAgentGroup(id string) (*domain.AgentGroup, error) {
-	return s.groupRepo.Get(context.Background(), id)
+func (s *AgentGroupService) GetAgentGroup(ctx context.Context, id string) (*domain.AgentGroup, error) {
+	return s.groupRepo.Get(ctx, id)
 }
 
 // CreateAgentGroup creates a new agent group with validation (handler interface method).
-func (s *AgentGroupService) CreateAgentGroup(group domain.AgentGroup) (*domain.AgentGroup, error) {
+func (s *AgentGroupService) CreateAgentGroup(ctx context.Context, group domain.AgentGroup) (*domain.AgentGroup, error) {
 	if err := validateAgentGroup(&group); err != nil {
 		return nil, err
 	}
@@ -74,12 +74,12 @@ func (s *AgentGroupService) CreateAgentGroup(group domain.AgentGroup) (*domain.A
 		group.UpdatedAt = now
 	}
 
-	if err := s.groupRepo.Create(context.Background(), &group); err != nil {
+	if err := s.groupRepo.Create(ctx, &group); err != nil {
 		return nil, fmt.Errorf("failed to create agent group: %w", err)
 	}
 
 	if s.auditService != nil {
-		if auditErr := s.auditService.RecordEvent(context.Background(), "api", domain.ActorTypeUser,
+		if auditErr := s.auditService.RecordEvent(ctx, "api", domain.ActorTypeUser,
 			"create_agent_group", "agent_group", group.ID, nil); auditErr != nil {
 			slog.Error("failed to record audit event", "error", auditErr)
 		}
@@ -89,18 +89,18 @@ func (s *AgentGroupService) CreateAgentGroup(group domain.AgentGroup) (*domain.A
 }
 
 // UpdateAgentGroup modifies an existing agent group (handler interface method).
-func (s *AgentGroupService) UpdateAgentGroup(id string, group domain.AgentGroup) (*domain.AgentGroup, error) {
+func (s *AgentGroupService) UpdateAgentGroup(ctx context.Context, id string, group domain.AgentGroup) (*domain.AgentGroup, error) {
 	if err := validateAgentGroup(&group); err != nil {
 		return nil, err
 	}
 
 	group.ID = id
-	if err := s.groupRepo.Update(context.Background(), &group); err != nil {
+	if err := s.groupRepo.Update(ctx, &group); err != nil {
 		return nil, fmt.Errorf("failed to update agent group: %w", err)
 	}
 
 	if s.auditService != nil {
-		if auditErr := s.auditService.RecordEvent(context.Background(), "api", domain.ActorTypeUser,
+		if auditErr := s.auditService.RecordEvent(ctx, "api", domain.ActorTypeUser,
 			"update_agent_group", "agent_group", id, nil); auditErr != nil {
 			slog.Error("failed to record audit event", "error", auditErr)
 		}
@@ -110,13 +110,13 @@ func (s *AgentGroupService) UpdateAgentGroup(id string, group domain.AgentGroup)
 }
 
 // DeleteAgentGroup removes an agent group (handler interface method).
-func (s *AgentGroupService) DeleteAgentGroup(id string) error {
-	if err := s.groupRepo.Delete(context.Background(), id); err != nil {
+func (s *AgentGroupService) DeleteAgentGroup(ctx context.Context, id string) error {
+	if err := s.groupRepo.Delete(ctx, id); err != nil {
 		return fmt.Errorf("failed to delete agent group: %w", err)
 	}
 
 	if s.auditService != nil {
-		if auditErr := s.auditService.RecordEvent(context.Background(), "api", domain.ActorTypeUser,
+		if auditErr := s.auditService.RecordEvent(ctx, "api", domain.ActorTypeUser,
 			"delete_agent_group", "agent_group", id, nil); auditErr != nil {
 			slog.Error("failed to record audit event", "error", auditErr)
 		}
@@ -126,8 +126,8 @@ func (s *AgentGroupService) DeleteAgentGroup(id string) error {
 }
 
 // ListMembers returns agents in a group.
-func (s *AgentGroupService) ListMembers(id string) ([]domain.Agent, int64, error) {
-	agents, err := s.groupRepo.ListMembers(context.Background(), id)
+func (s *AgentGroupService) ListMembers(ctx context.Context, id string) ([]domain.Agent, int64, error) {
+	agents, err := s.groupRepo.ListMembers(ctx, id)
 	if err != nil {
 		return nil, 0, fmt.Errorf("failed to list group members: %w", err)
 	}