diff --git a/frontend-modern/src/components/Settings/Settings.tsx b/frontend-modern/src/components/Settings/Settings.tsx
index 911476fd6..d51151a36 100644
--- a/frontend-modern/src/components/Settings/Settings.tsx
+++ b/frontend-modern/src/components/Settings/Settings.tsx
@@ -922,6 +922,21 @@ const Settings: Component = () => {
               <div>
                 <h3 class="text-lg font-semibold text-gray-800 dark:text-gray-200 mb-4">System Configuration</h3>
                 
+                {/* Environment Variable Info */}
+                <div class="mb-4 p-3 bg-blue-50 dark:bg-blue-900/20 border border-blue-200 dark:border-blue-700 rounded-lg">
+                  <div class="flex items-start gap-2">
+                    <svg class="w-5 h-5 text-blue-600 dark:text-blue-400 mt-0.5" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+                      <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z" />
+                    </svg>
+                    <div class="text-sm text-blue-800 dark:text-blue-200">
+                      <p class="font-medium mb-1">Configuration Sync:</p>
+                      <p>• Changes made here update both the database and .env file</p>
+                      <p>• If .env file exists at /etc/pulse/.env, it stays in sync with UI</p>
+                      <p>• System environment variables override both (if set)</p>
+                    </div>
+                  </div>
+                </div>
+                
                 <div class="space-y-4">
                   {/* Performance Settings */}
                   <div class="bg-gray-50 dark:bg-gray-700/50 rounded-lg p-4">
diff --git a/internal/config/persistence.go b/internal/config/persistence.go
index d9fb5e49b..958d543de 100644
--- a/internal/config/persistence.go
+++ b/internal/config/persistence.go
@@ -2,8 +2,10 @@ package config
 
 import (
 	"encoding/json"
+	"fmt"
 	"os"
 	"path/filepath"
+	"strconv"
 	"strings"
 	"sync"
 
@@ -376,11 +378,12 @@ func (c *ConfigPersistence) LoadNodesConfig() (*NodesConfig, error) {
 	return &config, nil
 }
 
-// SaveSystemSettings saves system settings to file
+// SaveSystemSettings saves system settings to both system.json and .env file
 func (c *ConfigPersistence) SaveSystemSettings(settings SystemSettings) error {
 	c.mu.Lock()
 	defer c.mu.Unlock()
 	
+	// Save to system.json for backwards compatibility
 	data, err := json.MarshalIndent(settings, "", "  ")
 	if err != nil {
 		return err
@@ -394,6 +397,13 @@ func (c *ConfigPersistence) SaveSystemSettings(settings SystemSettings) error {
 		return err
 	}
 	
+	// Also update .env file if it exists
+	envFile := filepath.Join(c.configDir, ".env")
+	if err := c.updateEnvFile(envFile, settings); err != nil {
+		log.Warn().Err(err).Msg("Failed to update .env file")
+		// Don't fail the operation if .env update fails
+	}
+	
 	log.Info().Str("file", c.systemFile).Msg("System settings saved")
 	return nil
 }
@@ -423,6 +433,104 @@ func (c *ConfigPersistence) LoadSystemSettings() (*SystemSettings, error) {
 	return &settings, nil
 }
 
+// updateEnvFile updates or creates .env file with system settings
+func (c *ConfigPersistence) updateEnvFile(envFile string, settings SystemSettings) error {
+	// Read existing .env file if it exists
+	envVars := make(map[string]string)
+	if data, err := os.ReadFile(envFile); err == nil {
+		lines := strings.Split(string(data), "\n")
+		for _, line := range lines {
+			line = strings.TrimSpace(line)
+			if line == "" || strings.HasPrefix(line, "#") {
+				continue
+			}
+			parts := strings.SplitN(line, "=", 2)
+			if len(parts) == 2 {
+				key := strings.TrimSpace(parts[0])
+				value := strings.TrimSpace(parts[1])
+				envVars[key] = value
+			}
+		}
+	}
+	
+	// Update with new values from settings
+	if settings.PollingInterval > 0 {
+		envVars["POLLING_INTERVAL"] = strconv.Itoa(settings.PollingInterval)
+	}
+	if settings.ConnectionTimeout > 0 {
+		envVars["CONNECTION_TIMEOUT"] = strconv.Itoa(settings.ConnectionTimeout)
+	}
+	if settings.UpdateChannel != "" {
+		envVars["UPDATE_CHANNEL"] = settings.UpdateChannel
+	}
+	envVars["AUTO_UPDATE_ENABLED"] = strconv.FormatBool(settings.AutoUpdateEnabled)
+	if settings.AutoUpdateCheckInterval > 0 {
+		envVars["AUTO_UPDATE_CHECK_INTERVAL"] = strconv.Itoa(settings.AutoUpdateCheckInterval)
+	}
+	if settings.AutoUpdateTime != "" {
+		envVars["AUTO_UPDATE_TIME"] = settings.AutoUpdateTime
+	}
+	if settings.AllowedOrigins != "" {
+		envVars["ALLOWED_ORIGINS"] = settings.AllowedOrigins
+	}
+	
+	// Build the new .env content
+	var content strings.Builder
+	content.WriteString("# Pulse Configuration File - Automatically updated by UI\n")
+	content.WriteString("# Changes made in the UI will be reflected here\n\n")
+	
+	// Write server settings
+	if port, ok := envVars["FRONTEND_PORT"]; ok {
+		content.WriteString(fmt.Sprintf("FRONTEND_PORT=%s\n", port))
+	}
+	if port, ok := envVars["BACKEND_PORT"]; ok {
+		content.WriteString(fmt.Sprintf("BACKEND_PORT=%s\n", port))
+	}
+	content.WriteString("\n")
+	
+	// Write monitoring settings
+	content.WriteString("# Monitoring\n")
+	if interval, ok := envVars["POLLING_INTERVAL"]; ok {
+		content.WriteString(fmt.Sprintf("POLLING_INTERVAL=%s\n", interval))
+	}
+	if timeout, ok := envVars["CONNECTION_TIMEOUT"]; ok {
+		content.WriteString(fmt.Sprintf("CONNECTION_TIMEOUT=%s\n", timeout))
+	}
+	content.WriteString("\n")
+	
+	// Write update settings
+	content.WriteString("# Updates\n")
+	if channel, ok := envVars["UPDATE_CHANNEL"]; ok {
+		content.WriteString(fmt.Sprintf("UPDATE_CHANNEL=%s\n", channel))
+	}
+	if enabled, ok := envVars["AUTO_UPDATE_ENABLED"]; ok {
+		content.WriteString(fmt.Sprintf("AUTO_UPDATE_ENABLED=%s\n", enabled))
+	}
+	if interval, ok := envVars["AUTO_UPDATE_CHECK_INTERVAL"]; ok {
+		content.WriteString(fmt.Sprintf("AUTO_UPDATE_CHECK_INTERVAL=%s\n", interval))
+	}
+	if time, ok := envVars["AUTO_UPDATE_TIME"]; ok {
+		content.WriteString(fmt.Sprintf("AUTO_UPDATE_TIME=%s\n", time))
+	}
+	content.WriteString("\n")
+	
+	// Write CORS settings
+	if origins, ok := envVars["ALLOWED_ORIGINS"]; ok && origins != "" {
+		content.WriteString("# CORS\n")
+		content.WriteString(fmt.Sprintf("ALLOWED_ORIGINS=%s\n", origins))
+		content.WriteString("\n")
+	}
+	
+	// Write logging settings if present
+	if level, ok := envVars["LOG_LEVEL"]; ok {
+		content.WriteString("# Logging\n")
+		content.WriteString(fmt.Sprintf("LOG_LEVEL=%s\n", level))
+	}
+	
+	// Write the file
+	return os.WriteFile(envFile, []byte(content.String()), 0644)
+}
+
 // Helper function
 func ptrFloat64(v float64) *float64 {
 	return &v