diff --git a/internal/command/mcp/config.go b/internal/command/mcp/config.go
index 991505e0cf..31e55fda82 100644
--- a/internal/command/mcp/config.go
+++ b/internal/command/mcp/config.go
@@ -567,8 +567,7 @@ func UpdateConfig(ctx context.Context, path string, configKey string, server str
 		return fmt.Errorf("failed to marshal updated configuration: %w", err)
 	}
 
-	err = os.WriteFile(path, updatedData, 0644)
-	if err != nil {
+	if err := writeConfigFile(path, updatedData); err != nil {
 		return fmt.Errorf("Failed to write updated configuration to %s: %v", path, err)
 	}
 
@@ -599,6 +598,17 @@ func runRemove(ctx context.Context) error {
 	return nil
 }
 
+// writeConfigFile writes an MCP client configuration readable only by its
+// owner, since the configuration can carry a Fly API token.
+func writeConfigFile(path string, data []byte) error {
+	if err := os.WriteFile(path, data, 0o600); err != nil {
+		return err
+	}
+	// os.WriteFile only applies perm on file creation; Chmod explicitly so
+	// the mode is applied on rewrite as well.
+	return os.Chmod(path, 0o600)
+}
+
 // removeConfig removes the MCP server from the configuration at the specified path
 func removeConfig(ctx context.Context, path string, configKey string, name string) error {
 	log := logger.FromContext(ctx)
@@ -654,8 +664,7 @@ func removeConfig(ctx context.Context, path string, configKey string, name strin
 		return fmt.Errorf("failed to marshal updated configuration: %w", err)
 	}
 
-	err = os.WriteFile(path, updatedData, 0644)
-	if err != nil {
+	if err := writeConfigFile(path, updatedData); err != nil {
 		return fmt.Errorf("Failed to write updated configuration to %s: %v", path, err)
 	}
 
diff --git a/internal/command/mcp/config_test.go b/internal/command/mcp/config_test.go
index c76d9de4dd..3536a50f45 100644
--- a/internal/command/mcp/config_test.go
+++ b/internal/command/mcp/config_test.go
@@ -1,7 +1,14 @@
 package mcp
 
 import (
+	"context"
+	"io"
+	"os"
+	"path/filepath"
+	"runtime"
 	"testing"
+
+	"github.com/superfly/flyctl/internal/logger"
 )
 
 func TestUnmarshalJSONC(t *testing.T) {
@@ -100,3 +107,67 @@ func TestUnmarshalJSONC(t *testing.T) {
 		}
 	})
 }
+
+func TestUpdateConfig_writesConfigAt0600_freshFile(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("file modes are not meaningful on windows")
+	}
+	path := filepath.Join(t.TempDir(), "client", "mcp.json")
+
+	if err := UpdateConfig(context.Background(), path, "", "flyctl", "flyctl", []string{"mcp", "server"}); err != nil {
+		t.Fatalf("UpdateConfig: %v", err)
+	}
+
+	info, err := os.Stat(path)
+	if err != nil {
+		t.Fatalf("stat config: %v", err)
+	}
+	if got, want := info.Mode().Perm(), os.FileMode(0o600); got != want {
+		t.Errorf("config mode = %o, want %o", got, want)
+	}
+}
+
+func TestUpdateConfig_appliesPermsToExistingFile(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("file modes are not meaningful on windows")
+	}
+	path := filepath.Join(t.TempDir(), "mcp.json")
+	if err := os.WriteFile(path, []byte(`{"mcpServers": {}}`), 0o644); err != nil {
+		t.Fatalf("seed config: %v", err)
+	}
+
+	if err := UpdateConfig(context.Background(), path, "", "flyctl", "flyctl", []string{"mcp", "server"}); err != nil {
+		t.Fatalf("UpdateConfig: %v", err)
+	}
+
+	info, err := os.Stat(path)
+	if err != nil {
+		t.Fatalf("stat config: %v", err)
+	}
+	if got, want := info.Mode().Perm(), os.FileMode(0o600); got != want {
+		t.Errorf("config mode = %o, want %o", got, want)
+	}
+}
+
+func TestRemoveConfig_appliesPermsToExistingFile(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("file modes are not meaningful on windows")
+	}
+	path := filepath.Join(t.TempDir(), "mcp.json")
+	if err := os.WriteFile(path, []byte(`{"mcpServers": {"flyctl": {"command": "flyctl"}}}`), 0o644); err != nil {
+		t.Fatalf("seed config: %v", err)
+	}
+	ctx := logger.NewContext(context.Background(), logger.New(io.Discard, logger.Error, false))
+
+	if err := removeConfig(ctx, path, "mcpServers", "flyctl"); err != nil {
+		t.Fatalf("removeConfig: %v", err)
+	}
+
+	info, err := os.Stat(path)
+	if err != nil {
+		t.Fatalf("stat config: %v", err)
+	}
+	if got, want := info.Mode().Perm(), os.FileMode(0o600); got != want {
+		t.Errorf("config mode = %o, want %o", got, want)
+	}
+}