diff --git a/internal/api/configapi/config_import_metadata_test.go b/internal/api/configapi/config_import_metadata_test.go
new file mode 100644
index 0000000000..c72130ab32
--- /dev/null
+++ b/internal/api/configapi/config_import_metadata_test.go
@@ -0,0 +1,119 @@
+package configapi
+
+import (
+	"bytes"
+	"encoding/json"
+	"net/http"
+	"net/http/httptest"
+	"os"
+	"path/filepath"
+	"reflect"
+	"testing"
+	"time"
+
+	"github.com/rcourtman/pulse-go-rewrite/internal/config"
+)
+
+func TestHandleImportConfigMetadataFailureDoesNotApplyOrSucceed(t *testing.T) {
+	for _, failure := range []string{"metadata_directory", "closed_store"} {
+		t.Run(failure, func(t *testing.T) {
+			const passphrase = "synthetic-import-validation-passphrase"
+			cfg := &config.Config{DataPath: t.TempDir(), PublicURL: "https://keep.invalid", AuthUser: "keep-admin", AuthPass: "synthetic-auth-hash"}
+			p := config.NewConfigPersistence(cfg.DataPath)
+			settings := config.DefaultSystemSettings()
+			settings.PublicURL = cfg.PublicURL
+			if err := p.SaveSystemSettings(*settings); err != nil {
+				t.Fatal(err)
+			}
+			if err := p.SaveAPITokens([]config.APITokenRecord{{ID: "keep-token", Hash: "synthetic-token-hash", OrgID: "default"}}); err != nil {
+				t.Fatal(err)
+			}
+			if err := os.WriteFile(filepath.Join(cfg.DataPath, ".env"), []byte("AUTO_UPDATE_ENABLED=true\nPOLLING_INTERVAL=77\n"), 0600); err != nil {
+				t.Fatal(err)
+			}
+			store := p.GetGuestMetadataStore()
+			if err := store.Set("keep:101", &config.GuestMetadata{Description: "Retained operator metadata"}); err != nil {
+				t.Fatal(err)
+			}
+			metadataBefore := store.GetAll()
+			if failure == "closed_store" {
+				if err := store.Close(time.Second); err != nil {
+					t.Fatal(err)
+				}
+			} else {
+				metadataPath := filepath.Join(cfg.DataPath, "guest_metadata.json")
+				if err := os.Remove(metadataPath); err != nil {
+					t.Fatal(err)
+				}
+				if err := os.Mkdir(metadataPath, 0700); err != nil {
+					t.Fatal(err)
+				}
+			}
+			before := metadataImportFiles(t, cfg.DataPath)
+			beforeConfig := cfg.DeepCopy()
+			reloads, audits := 0, 0
+			h := &ConfigHandlers{defaultConfig: cfg, defaultPersistence: p, reloadFunc: func() error { reloads++; return nil }}
+			h.SetRuntimeDependencies(RuntimeDependencies{AuditEvent: func(_, event, _, _, _ string, success bool, _ string) {
+				audits++
+				if event != "config_imported" || success {
+					t.Error("failed metadata import produced a success audit")
+				}
+			}})
+			plaintext, err := json.Marshal(map[string]any{
+				"version": "4.4", "nodes": map[string]any{}, "alerts": map[string]any{},
+				"email": map[string]any{}, "webhooks": nil, "system": map[string]any{},
+				"guestMetadata": map[string]any{"imported:202": map[string]string{"description": failure}},
+			})
+			if err != nil {
+				t.Fatal(err)
+			}
+			request := ImportConfigRequest{Data: encryptedImportValidationFixture(t, plaintext, passphrase), Passphrase: passphrase}
+			body, err := json.Marshal(request)
+			if err != nil {
+				t.Fatal(err)
+			}
+			rec := httptest.NewRecorder()
+			h.HandleImportConfig(rec, httptest.NewRequest(http.MethodPost, "/api/config/import", bytes.NewReader(body)))
+			if rec.Code != http.StatusBadRequest || rec.Body.String() != "Failed to import configuration. Verify the backup file and passphrase are correct.\n" {
+				t.Fatalf("failed metadata import response = %d %q", rec.Code, rec.Body.String())
+			}
+			if reloads != 0 || audits != 1 || !reflect.DeepEqual(beforeConfig, cfg.DeepCopy()) {
+				t.Error("failed import changed runtime or triggered apply")
+			}
+			if !reflect.DeepEqual(before, metadataImportFiles(t, cfg.DataPath)) || !reflect.DeepEqual(metadataBefore, store.GetAll()) {
+				t.Error("failed import changed persisted or live state")
+			}
+			readback, err := json.Marshal(map[string]any{"request": request, "status": rec.Code, "contentType": rec.Header().Get("Content-Type"), "body": rec.Body.String()})
+			if err != nil {
+				t.Fatal(err)
+			}
+			t.Logf("SYNTHETIC_METADATA_IMPORT_REJECTION_READBACK %s", readback)
+		})
+	}
+}
+
+func metadataImportFiles(t *testing.T, dir string) map[string]string {
+	t.Helper()
+	files := make(map[string]string)
+	if err := filepath.WalkDir(dir, func(path string, entry os.DirEntry, err error) error {
+		if err != nil {
+			return err
+		}
+		info, err := entry.Info()
+		if err != nil {
+			return err
+		}
+		files[path] = info.Mode().String()
+		if !entry.IsDir() {
+			data, err := os.ReadFile(path)
+			if err != nil {
+				return err
+			}
+			files[path] += string(data)
+		}
+		return nil
+	}); err != nil {
+		t.Fatal(err)
+	}
+	return files
+}
diff --git a/internal/config/export.go b/internal/config/export.go
index 26da1b366d..cd90fd08c5 100644
--- a/internal/config/export.go
+++ b/internal/config/export.go
@@ -258,15 +258,13 @@ func (c *ConfigPersistence) ImportConfig(encryptedData string, passphrase string
 		}
 	}
 
-	if err := tx.Commit(); err != nil {
+	if err := c.GetGuestMetadataStore().commitImport(tx, exportData.GuestMetadata); err != nil {
 		return fmt.Errorf("failed to commit import transaction: %w", err)
 	}
 	committed = true
-
-	// Import guest metadata into the active persistence scope.
-	if err := c.GetGuestMetadataStore().ReplaceAll(exportData.GuestMetadata); err != nil {
-		log.Warn().Err(err).Msg("Failed to import guest metadata")
-	}
+	c.mu.Lock()
+	c.cleanupOldBackups(c.nodesFile + ".backup-*")
+	c.mu.Unlock()
 
 	return nil
 }
diff --git a/internal/config/export_metadata_transaction_test.go b/internal/config/export_metadata_transaction_test.go
new file mode 100644
index 0000000000..d917749ddd
--- /dev/null
+++ b/internal/config/export_metadata_transaction_test.go
@@ -0,0 +1,178 @@
+package config
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+	"path/filepath"
+	"reflect"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/rcourtman/pulse-go-rewrite/internal/notifications"
+)
+
+func metadataImportArchive(t *testing.T, metadata map[string]*GuestMetadata) string {
+	t.Helper()
+	settings := DefaultSystemSettings()
+	settings.PublicURL = "https://imported.invalid"
+	data, err := json.Marshal(ExportData{
+		Version: "4.4", System: *settings,
+		Email:         notifications.EmailConfig{SMTPHost: "imported.invalid", Password: "synthetic-imported-secret"},
+		APITokens:     []APITokenRecord{{ID: "imported-token", Hash: "synthetic-imported-hash", OrgID: "default"}},
+		GuestMetadata: metadata,
+	})
+	if err != nil {
+		t.Fatal(err)
+	}
+	return encryptImportValidationData(t, data)
+}
+
+func TestImportConfigMetadataFailurePreservesState(t *testing.T) {
+	for _, failure := range []string{"metadata_directory", "closed_store", "later_destination", "later_destination_without_metadata_file"} {
+		t.Run(failure, func(t *testing.T) {
+			cp := seedImportValidationState(t)
+			seedMetadataImportRecoveryArtifacts(t, cp)
+			store := cp.GetGuestMetadataStore()
+			metadataBefore := store.GetAll()
+			metadataFile := filepath.Join(cp.configDir, "guest_metadata.json")
+			var blocker string
+			switch failure {
+			case "metadata_directory":
+				blocker = metadataFile
+			case "closed_store":
+				if err := store.Close(time.Second); err != nil {
+					t.Fatal(err)
+				}
+			case "later_destination_without_metadata_file":
+				if err := os.Remove(metadataFile); err != nil {
+					t.Fatal(err)
+				}
+				blocker = cp.systemFile
+			case "later_destination":
+				blocker = cp.systemFile
+			}
+			if blocker != "" {
+				if err := os.Remove(blocker); err != nil {
+					t.Fatal(err)
+				}
+				if err := os.Mkdir(blocker, 0700); err != nil {
+					t.Fatal(err)
+				}
+				if err := os.WriteFile(filepath.Join(blocker, "keep"), []byte("retained blocker"), 0600); err != nil {
+					t.Fatal(err)
+				}
+			}
+			before := importValidationFiles(t, cp.configDir)
+			err := cp.ImportConfig(metadataImportArchive(t, map[string]*GuestMetadata{
+				"imported:202": {Description: "Imported metadata", Tags: []string{"imported"}},
+			}), "synthetic-import-validation-passphrase")
+			if err == nil {
+				t.Error("failed metadata recovery was reported as successful")
+			}
+			if !reflect.DeepEqual(before, importValidationFiles(t, cp.configDir)) {
+				t.Error("failed import changed files, credentials or transaction artifacts")
+			}
+			if !reflect.DeepEqual(metadataBefore, store.GetAll()) {
+				t.Error("failed import replaced live metadata")
+			}
+		})
+	}
+}
+
+func TestImportConfigCommitsMetadataWithConfiguration(t *testing.T) {
+	for _, inventory := range []string{"nil", "empty", "populated"} {
+		t.Run(inventory, func(t *testing.T) {
+			cp := seedImportValidationState(t)
+			seedMetadataImportRecoveryArtifacts(t, cp)
+			nodesBefore, err := os.ReadFile(cp.nodesFile)
+			if err != nil {
+				t.Fatal(err)
+			}
+			tokensBefore, err := os.ReadFile(cp.apiTokensFile)
+			if err != nil {
+				t.Fatal(err)
+			}
+			var metadata map[string]*GuestMetadata
+			expected := map[string]*GuestMetadata{}
+			if inventory == "empty" {
+				metadata = map[string]*GuestMetadata{}
+			}
+			if inventory == "populated" {
+				metadata = map[string]*GuestMetadata{
+					"imported:202": {ID: "wrong-id", Description: "Imported description", Notes: []string{"retained note"}},
+					"null-entry":   nil,
+				}
+				expected["imported:202"] = &GuestMetadata{ID: "imported:202", Description: "Imported description", Notes: []string{"retained note"}, Tags: []string{}}
+			}
+			if err := cp.ImportConfig(metadataImportArchive(t, metadata), "synthetic-import-validation-passphrase"); err != nil {
+				t.Fatal(err)
+			}
+			for path, want := range map[string][]byte{cp.nodesFile + ".backup": nodesBefore, cp.apiTokensFile + ".backup": tokensBefore} {
+				if got, err := os.ReadFile(path); err != nil || string(got) != string(want) {
+					t.Error("successful import did not retain its previous configuration backup")
+				}
+			}
+			backups, err := filepath.Glob(cp.nodesFile + ".backup-*")
+			if err != nil || len(backups) != 10 {
+				t.Fatal("successful import did not apply the existing ten-backup retention")
+			}
+			env, err := os.ReadFile(filepath.Join(cp.configDir, ".env"))
+			if err != nil || strings.Contains(string(env), "POLLING_INTERVAL=") || !strings.Contains(string(env), "AUTO_UPDATE_ENABLED=false") || !strings.Contains(string(env), "KEEP_SETTING=retained") {
+				t.Fatal("successful import did not commit the existing legacy settings-file update")
+			}
+			if !reflect.DeepEqual(cp.GetGuestMetadataStore().GetAll(), expected) {
+				t.Error("successful import did not publish normalized metadata")
+			}
+			reloaded := NewGuestMetadataStore(cp.configDir, nil)
+			if !reflect.DeepEqual(reloaded.GetAll(), expected) {
+				t.Error("fresh metadata reader does not match the imported live state")
+			}
+			if err := cp.GetGuestMetadataStore().Load(); err != nil {
+				t.Fatalf("committed metadata cannot be reloaded: %v", err)
+			}
+			settings, err := cp.LoadSystemSettings()
+			if err != nil || settings.PublicURL != "https://imported.invalid" {
+				t.Fatal("successful import did not persist settings")
+			}
+			tokens, err := cp.LoadAPITokens()
+			if err != nil || len(tokens) != 1 || tokens[0].ID != "imported-token" {
+				t.Fatal("successful import did not persist credentials")
+			}
+			info, err := os.Stat(filepath.Join(cp.configDir, "guest_metadata.json"))
+			if err != nil || info.Mode().Perm() != 0600 {
+				t.Fatal("imported metadata is not a private file")
+			}
+			for path := range importValidationFiles(t, cp.configDir) {
+				if strings.HasPrefix(filepath.Base(path), ".import-") || strings.Contains(filepath.Base(path), ".import-backup-") {
+					t.Error("successful import retained transaction staging")
+				}
+			}
+		})
+	}
+}
+
+func seedMetadataImportRecoveryArtifacts(t *testing.T, cp *ConfigPersistence) {
+	t.Helper()
+	for path, data := range map[string]string{
+		filepath.Join(cp.configDir, ".env"): "UPDATE_CHANNEL=stable\nAUTO_UPDATE_ENABLED=true\nPOLLING_INTERVAL=77\nKEEP_SETTING=retained\n",
+		cp.nodesFile + ".backup":            "prior node backup",
+		cp.apiTokensFile + ".backup":        "prior token backup",
+	} {
+		if err := os.WriteFile(path, []byte(data), 0600); err != nil {
+			t.Fatal(err)
+		}
+	}
+	// More than the normal retention bound makes premature pruning visible.
+	for i := 0; i < 11; i++ {
+		path := fmt.Sprintf("%s.backup-20260101-%06d", cp.nodesFile, i)
+		if err := os.WriteFile(path, []byte(fmt.Sprintf("retained backup %d", i)), 0600); err != nil {
+			t.Fatal(err)
+		}
+		stamp := time.Date(2000, 1, 1, 0, i, 0, 0, time.UTC)
+		if err := os.Chtimes(path, stamp, stamp); err != nil {
+			t.Fatal(err)
+		}
+	}
+}
diff --git a/internal/config/guest_metadata_import.go b/internal/config/guest_metadata_import.go
new file mode 100644
index 0000000000..afd4b8bd6d
--- /dev/null
+++ b/internal/config/guest_metadata_import.go
@@ -0,0 +1,52 @@
+package config
+
+import (
+	"encoding/json"
+	"fmt"
+	"path/filepath"
+)
+
+// commitImport includes guest metadata in the same file transaction as settings
+// and credentials. Keep the store's writer and mutation locks through commit so
+// an older background snapshot cannot overwrite the imported file, and readers
+// cannot observe imported metadata before its configuration has committed.
+func (s *GuestMetadataStore) commitImport(tx *importTransaction, metadata map[string]*GuestMetadata) error {
+	s.writeMu.Lock()
+	defer s.writeMu.Unlock()
+	s.mu.Lock()
+	defer s.mu.Unlock()
+	if s.closed.Load() {
+		return ErrGuestMetadataStoreClosed
+	}
+
+	working := make(map[string]*GuestMetadata, len(metadata))
+	for id, meta := range metadata {
+		if meta == nil {
+			continue
+		}
+		clone := cloneGuestMetadata(meta)
+		clone.ID = id
+		if clone.Tags == nil {
+			clone.Tags = []string{}
+		}
+		working[id] = clone
+	}
+	data, err := json.Marshal(working)
+	if err != nil {
+		return fmt.Errorf("serialize imported guest metadata: %w", err)
+	}
+	if err := tx.StageFile(filepath.Join(s.dataPath, "guest_metadata.json"), data, 0600); err != nil {
+		return fmt.Errorf("stage imported guest metadata: %w", err)
+	}
+	if err := tx.Commit(); err != nil {
+		return err
+	}
+
+	// Publish only after every file committed. A pending writer will now see
+	// that this revision is durable instead of replaying a pre-import snapshot.
+	s.metadata = working
+	s.revision++
+	s.attemptedRevision = s.revision
+	s.lastWriteErr = nil
+	return nil
+}
diff --git a/internal/config/guest_metadata_import_test.go b/internal/config/guest_metadata_import_test.go
new file mode 100644
index 0000000000..433b51ba88
--- /dev/null
+++ b/internal/config/guest_metadata_import_test.go
@@ -0,0 +1,134 @@
+package config
+
+import (
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"reflect"
+	"sync"
+	"testing"
+	"time"
+)
+
+type importBlockedMetadataFS struct {
+	FileSystem
+	once    sync.Once
+	entered chan struct{}
+	release chan struct{}
+}
+
+func (f *importBlockedMetadataFS) WriteFile(path string, data []byte, perm os.FileMode) error {
+	if filepath.Base(path) == "guest_metadata.json.tmp" {
+		f.once.Do(func() { close(f.entered); <-f.release })
+	}
+	return f.FileSystem.WriteFile(path, data, perm)
+}
+
+func TestGuestMetadataImportOrdersPendingSnapshotsAndCopiesInput(t *testing.T) {
+	dir := t.TempDir()
+	fs := &importBlockedMetadataFS{FileSystem: defaultFileSystem{}, entered: make(chan struct{}), release: make(chan struct{})}
+	store := NewGuestMetadataStore(dir, fs)
+	var releaseOnce sync.Once
+	release := func() { releaseOnce.Do(func() { close(fs.release) }) }
+	t.Cleanup(func() {
+		release()
+		if err := store.Close(time.Second); err != nil {
+			t.Error(err)
+		}
+	})
+	if err := store.SetAsync("old:101", &GuestMetadata{Description: "Old snapshot"}); err != nil {
+		t.Fatal(err)
+	}
+	select {
+	case <-fs.entered:
+	case <-time.After(time.Second):
+		t.Fatal("pending metadata writer did not enter")
+	}
+	if err := store.RememberIdentity("old:101", "Old guest", "qemu"); err != nil {
+		t.Fatal(err)
+	}
+	tx, err := newImportTransaction(dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer tx.Cleanup()
+	settings := filepath.Join(dir, "system.json")
+	if err := os.WriteFile(settings, []byte("old settings"), 0600); err != nil {
+		t.Fatal(err)
+	}
+	if err := tx.StageFile(settings, []byte("imported settings"), 0600); err != nil {
+		t.Fatal(err)
+	}
+	metadata := map[string]*GuestMetadata{"new:202": {ID: "wrong", Description: "Imported snapshot", Tags: []string{"imported"}, Notes: []string{"note"}}}
+	done := make(chan error, 1)
+	go func() { done <- store.commitImport(tx, metadata) }()
+	select {
+	case err := <-done:
+		t.Fatalf("import overtook an in-flight metadata snapshot: %v", err)
+	case <-time.After(50 * time.Millisecond):
+		// A bounded negative observation, followed by the positive joined proof.
+	}
+	if data, err := os.ReadFile(settings); err != nil || string(data) != "old settings" {
+		t.Fatal("configuration committed while the old metadata write was still in flight")
+	}
+	release()
+	select {
+	case err := <-done:
+		if err != nil {
+			t.Fatal(err)
+		}
+	case <-time.After(5 * time.Second):
+		t.Fatal("import did not complete after the prior snapshot")
+	}
+	if !store.WaitForPendingWrites(time.Second) {
+		t.Fatal("pending writer did not drain")
+	}
+	expected := map[string]*GuestMetadata{"new:202": {ID: "new:202", Description: "Imported snapshot", Tags: []string{"imported"}, Notes: []string{"note"}}}
+	metadata["new:202"].Tags[0] = "caller mutation"
+	metadata["new:202"].Notes[0] = "caller mutation"
+	if !reflect.DeepEqual(store.GetAll(), expected) {
+		t.Fatal("import retained old records or caller-owned slices")
+	}
+	data, err := os.ReadFile(filepath.Join(dir, "guest_metadata.json"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	var persisted map[string]*GuestMetadata
+	if err := json.Unmarshal(data, &persisted); err != nil {
+		t.Fatal(err)
+	}
+	if !reflect.DeepEqual(persisted, expected) {
+		t.Fatal("pending snapshot overwrote the imported metadata file")
+	}
+	if data, err := os.ReadFile(settings); err != nil || string(data) != "imported settings" {
+		t.Fatal("metadata import did not commit its settings")
+	}
+	if err := store.Load(); err != nil {
+		t.Fatalf("committed revision was left pending: %v", err)
+	}
+}
+
+func TestGuestMetadataImportStageFailurePreservesMemory(t *testing.T) {
+	cp := seedImportValidationState(t)
+	store := cp.GetGuestMetadataStore()
+	before := store.GetAll()
+	tx, err := newImportTransaction(cp.configDir)
+	if err != nil {
+		t.Fatal(err)
+	}
+	// An occupied staging pathname is an actual filesystem failure before
+	// commit, not a simulated successful persistence result.
+	if err := os.Remove(tx.stagingDir); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(tx.stagingDir, []byte("block staging"), 0600); err != nil {
+		t.Fatal(err)
+	}
+	defer tx.Cleanup()
+	if err := store.commitImport(tx, map[string]*GuestMetadata{"new:202": {Description: "Do not publish"}}); err == nil {
+		t.Fatal("metadata staging failure was accepted")
+	}
+	if !reflect.DeepEqual(before, store.GetAll()) || tx.committed {
+		t.Fatal("staging failure changed live metadata or committed configuration")
+	}
+}
diff --git a/internal/config/import_transaction.go b/internal/config/import_transaction.go
index 81949b9e0e..d8d85fe2c8 100644
--- a/internal/config/import_transaction.go
+++ b/internal/config/import_transaction.go
@@ -170,6 +170,12 @@ func (tx *importTransaction) Commit() error {
 					continue
 				}
 				tx.backups[target] = ""
+			} else {
+				// This target did not exist before the import. Restoring its
+				// absence matters just as much as restoring an overwritten file.
+				if err := os.Remove(target); err != nil && !os.IsNotExist(err) {
+					joinRestoreErr(fmt.Errorf("remove new target %s during restore: %w", target, err))
+				}
 			}
 		}
 		return restoreErr
@@ -203,11 +209,12 @@ func (tx *importTransaction) Commit() error {
 			return failWithRestore(fmt.Errorf("stat destination %s: %w", target, err))
 		}
 
+		// Track the target before replacement: a failed rename after moving
+		// the original into a backup must restore that original too.
+		applied = append(applied, target)
 		if err := os.Rename(stagedPath, target); err != nil {
 			return failWithRestore(fmt.Errorf("apply staged file to %s: %w", target, err))
 		}
-
-		applied = append(applied, target)
 	}
 
 	// Successful commit: remove backups. Keep success behavior, but surface cleanup failures in logs.
diff --git a/internal/config/import_transaction_restore_test.go b/internal/config/import_transaction_restore_test.go
new file mode 100644
index 0000000000..b978a6033a
--- /dev/null
+++ b/internal/config/import_transaction_restore_test.go
@@ -0,0 +1,68 @@
+package config
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+// Failed replacement must restore both overwritten files and the absence of
+// files first created by this transaction, before returning to its caller.
+func TestImportTransactionFailedCommitRestoresEveryTarget(t *testing.T) {
+	for _, failure := range []string{"later_directory", "missing_staged_existing", "missing_staged_new"} {
+		t.Run(failure, func(t *testing.T) {
+			dir := t.TempDir()
+			existing := filepath.Join(dir, "a-existing")
+			created := filepath.Join(dir, "b-new")
+			blocked := filepath.Join(dir, "z-directory")
+			if err := os.WriteFile(existing, []byte("original"), 0640); err != nil {
+				t.Fatal(err)
+			}
+			if err := os.Mkdir(blocked, 0700); err != nil {
+				t.Fatal(err)
+			}
+			tx, err := newImportTransaction(dir)
+			if err != nil {
+				t.Fatal(err)
+			}
+			defer tx.Cleanup()
+			for _, target := range []string{existing, created, blocked} {
+				if err := tx.StageFile(target, []byte("replacement"), 0600); err != nil {
+					t.Fatal(err)
+				}
+			}
+			if failure != "later_directory" {
+				target := existing
+				if failure == "missing_staged_new" {
+					target = created
+				}
+				if err := os.Remove(tx.staged[target]); err != nil {
+					t.Fatal(err)
+				}
+			}
+			if err := tx.Commit(); err == nil {
+				t.Fatal("expected failed commit")
+			}
+			assertRestored := func() {
+				t.Helper()
+				data, err := os.ReadFile(existing)
+				if err != nil || string(data) != "original" {
+					t.Error("failed commit did not restore the original file")
+				}
+				info, err := os.Stat(existing)
+				if err != nil || info.Mode().Perm() != 0640 {
+					t.Error("failed commit did not restore original permissions")
+				}
+				if _, err := os.Stat(created); !os.IsNotExist(err) {
+					t.Error("failed commit left a newly created configuration file")
+				}
+				if info, err := os.Stat(blocked); err != nil || !info.IsDir() {
+					t.Error("failed commit changed the blocking directory")
+				}
+			}
+			assertRestored()
+			tx.Rollback()
+			assertRestored()
+		})
+	}
+}
diff --git a/internal/config/persistence.go b/internal/config/persistence.go
index 354698ae54..0963246f98 100644
--- a/internal/config/persistence.go
+++ b/internal/config/persistence.go
@@ -473,6 +473,16 @@ func (c *ConfigPersistence) writeConfigFileLocked(path string, data []byte, perm
 	return nil
 }
 
+// writeConfigBackupLocked preserves ordinary backup writes, but makes them
+// part of an active import instead of changing recovery files before commit.
+// Caller must hold c.mu.
+func (c *ConfigPersistence) writeConfigBackupLocked(path string, data []byte, perm os.FileMode) error {
+	if c.tx != nil {
+		return c.tx.StageFile(path, data, perm)
+	}
+	return c.fs.WriteFile(path, data, perm)
+}
+
 // preserveCorruptConfigFileLocked moves a config file that failed to parse or
 // decrypt aside to <path>.corrupt-<timestamp>. Loaders return empty data with
 // a nil error for such files, so read-modify-write savers would otherwise
@@ -782,7 +792,7 @@ func (c *ConfigPersistence) persistAPITokensLocked(tokens []APITokenRecord) erro
 
 	// Backup previous state (best effort).
 	if existing, err := c.fs.ReadFile(c.apiTokensFile); err == nil && len(existing) > 0 {
-		if err := c.fs.WriteFile(c.apiTokensFile+".backup", existing, 0600); err != nil {
+		if err := c.writeConfigBackupLocked(c.apiTokensFile+".backup", existing, 0600); err != nil {
 			log.Warn().Err(err).Msg("Failed to create API token backup file")
 		}
 	}
@@ -1634,7 +1644,7 @@ func (c *ConfigPersistence) saveNodesConfig(pveInstances []PVEInstance, pbsInsta
 		// Create timestamped backup
 		timestampedBackup := fmt.Sprintf("%s.backup-%s", c.nodesFile, time.Now().Format("20060102-150405"))
 		if backupData, err := c.fs.ReadFile(c.nodesFile); err == nil {
-			if err := c.fs.WriteFile(timestampedBackup, backupData, 0600); err != nil {
+			if err := c.writeConfigBackupLocked(timestampedBackup, backupData, 0600); err != nil {
 				log.Warn().Err(err).Msg("Failed to create timestamped backup of nodes config")
 			} else {
 				log.Info().Str("backup", timestampedBackup).Msg("Created timestamped backup of nodes config")
@@ -1644,13 +1654,16 @@ func (c *ConfigPersistence) saveNodesConfig(pveInstances []PVEInstance, pbsInsta
 		// Also maintain a "latest" backup for quick recovery
 		latestBackup := c.nodesFile + ".backup"
 		if backupData, err := c.fs.ReadFile(c.nodesFile); err == nil {
-			if err := c.fs.WriteFile(latestBackup, backupData, 0600); err != nil {
+			if err := c.writeConfigBackupLocked(latestBackup, backupData, 0600); err != nil {
 				log.Warn().Err(err).Msg("Failed to create latest backup of nodes config")
 			}
 		}
 
-		// Clean up old timestamped backups (keep last 10)
-		c.cleanupOldBackups(c.nodesFile + ".backup-*")
+		// Imports prune only after the entire archive commits. A failed
+		// recovery must not delete an older, still usable backup.
+		if c.tx == nil {
+			c.cleanupOldBackups(c.nodesFile + ".backup-*")
+		}
 	}
 
 	// Encrypt if crypto manager is available
@@ -2037,6 +2050,9 @@ func (c *ConfigPersistence) saveSystemSettingsLocked(settings SystemSettings) er
 	// Also update the .env file if it exists
 	envFile := filepath.Join(c.configDir, ".env")
 	if err := c.updateEnvFile(envFile, settings); err != nil {
+		if c.tx != nil {
+			return fmt.Errorf("stage imported environment settings: %w", err)
+		}
 		log.Warn().Err(err).Msg("Failed to update .env file")
 		// Don't fail the operation if .env update fails
 	}
@@ -3877,6 +3893,9 @@ func (c *ConfigPersistence) updateEnvFile(envFile string, settings SystemSetting
 			perm = 0600
 		}
 	}
+	if c.tx != nil {
+		return c.writeConfigFileLocked(envFile, []byte(content), perm)
+	}
 	if err := c.fs.WriteFile(tempFile, []byte(content), perm); err != nil {
 		return fmt.Errorf("write temp env file %s: %w", tempFile, err)
 	}