diff --git a/internal/config/manager.go b/internal/config/manager.go
index 0ade56d..0b69ad2 100644
--- a/internal/config/manager.go
+++ b/internal/config/manager.go
@@ -72,6 +72,11 @@ type ConfigMcp struct {
 	//   true            -> global_mcp_config_file   (user-global)
 	Global bool           `yaml:"global,omitempty" json:"global,omitempty"  jsonschema:"description=When true the MCP is configured in the agent's global config file instead of the project-scoped one"`
 	Merge  *bool          `yaml:"merge,omitempty"  json:"merge,omitempty"   jsonschema:"description=Merge server entry into existing file rather than overwriting it (default: true when omitted)"`
+	// Prune opts this entry's target file in for `gaal sync --prune`.
+	// Default false — without this gate, --prune was destructive even
+	// against agent config files holding entries the user added by hand
+	// outside of gaal. See #142.
+	Prune  bool           `yaml:"prune,omitempty"  json:"prune,omitempty"   jsonschema:"description=Allow gaal sync --prune to remove orphan entries from this MCP target file (default: false)"`
 	Inline *ConfigMcpItem `yaml:"inline,omitempty" json:"inline,omitempty"  jsonschema:"description=Inline server definition (mutually exclusive with source)"                          validate:"omitempty"`
 }
 
diff --git a/internal/mcp/manager.go b/internal/mcp/manager.go
index 43f22a5..13da0e2 100644
--- a/internal/mcp/manager.go
+++ b/internal/mcp/manager.go
@@ -305,23 +305,36 @@ func mergeIntoTarget(target, name string, entry serverEntry) error {
 	return nil
 }
 
-// Prune removes mcpServers entries from each managed target file whose names
-// are no longer declared in the config for that target. Entries added manually
-// outside of gaal are also removed — callers should only use --prune on files
-// they intend to manage exclusively with gaal.
+// Prune removes mcpServers entries from each managed target file whose
+// names are no longer declared in the config for that target.
+//
+// Per #142, this is gated by an opt-in flag: a target is only pruned
+// when at least one ConfigMcp entry pointing at it sets `prune: true`.
+// Without that gate `--prune` could silently wipe MCP entries the user
+// had added by hand to a shared file (e.g. claude-code's ~/.claude.json,
+// codex's ~/.codex/config.toml).
 func (m *Manager) Prune(ctx context.Context) error {
 	slog.DebugContext(ctx, "pruning orphan mcp entries")
 
-	// Build expected name set per target path.
+	// Build expected name set + per-target prune-opt-in.
 	keepPerTarget := make(map[string]map[string]struct{})
+	pruneTarget := make(map[string]bool)
 	for _, mc := range m.resolvedMCPs() {
 		if keepPerTarget[mc.Target] == nil {
 			keepPerTarget[mc.Target] = make(map[string]struct{})
 		}
 		keepPerTarget[mc.Target][mc.Name] = struct{}{}
+		if mc.Prune {
+			pruneTarget[mc.Target] = true
+		}
 	}
 
 	for target, keep := range keepPerTarget {
+		if !pruneTarget[target] {
+			slog.Debug("mcp prune: target not opted in (set prune: true on at least one entry)",
+				"target", target)
+			continue
+		}
 		codec := codecFor(target)
 		servers, err := codec.ReadServers(target)
 		if err != nil {
diff --git a/internal/mcp/manager_test.go b/internal/mcp/manager_test.go
index 9fb2f68..c3a5883 100644
--- a/internal/mcp/manager_test.go
+++ b/internal/mcp/manager_test.go
@@ -718,9 +718,11 @@ func TestMCPPrune_RemovesOrphanEntry(t *testing.T) {
 	initial := `{"mcpServers":{"kept":{"command":"node"},"orphan":{"command":"python"}}}`
 	os.WriteFile(target, []byte(initial), 0o644)
 
-	// Config only declares "kept".
+	// Config only declares "kept" — and opts the target in to pruning
+	// per #142 (without prune: true on at least one entry, the target
+	// is not eligible for orphan removal even when --prune is passed).
 	cfg := []config.ConfigMcp{
-		{Name: "kept", Target: target, Inline: &config.ConfigMcpItem{Command: "node"}},
+		{Name: "kept", Target: target, Prune: true, Inline: &config.ConfigMcpItem{Command: "node"}},
 	}
 	m := NewManager(cfg, "", "")
 	if err := m.Prune(context.Background()); err != nil {