diff --git a/cmd/kpod/common.go b/cmd/kpod/common.go
index 6d1f5299..d9aab97a 100644
--- a/cmd/kpod/common.go
+++ b/cmd/kpod/common.go
@@ -10,6 +10,10 @@ import (
 	"github.com/urfave/cli"
 )
 
+var (
+	stores = make(map[storage.Store]struct{})
+)
+
 func getStore(c *libkpod.Config) (storage.Store, error) {
 	options := storage.DefaultStoreOptions
 	options.GraphRoot = c.Root
@@ -22,9 +26,18 @@ func getStore(c *libkpod.Config) (storage.Store, error) {
 		return nil, err
 	}
 	is.Transport.SetStore(store)
+	stores[store] = struct{}{}
 	return store, nil
 }
 
+func shutdownStores() {
+	for store := range stores {
+		if _, err := store.Shutdown(false); err != nil {
+			break
+		}
+	}
+}
+
 func getConfig(c *cli.Context) (*libkpod.Config, error) {
 	config := libkpod.DefaultConfig()
 	if c.GlobalIsSet("config") {
diff --git a/cmd/kpod/diff.go b/cmd/kpod/diff.go
index f8592e71..fa8c1d56 100644
--- a/cmd/kpod/diff.go
+++ b/cmd/kpod/diff.go
@@ -86,6 +86,7 @@ func diffCmd(c *cli.Context) error {
 	if err != nil {
 		return errors.Wrapf(err, "could not get container server")
 	}
+	defer server.Shutdown()
 
 	to := c.Args().Get(0)
 	changes, err := server.GetDiff("", to)
diff --git a/cmd/kpod/inspect.go b/cmd/kpod/inspect.go
index fe8d53b7..5371a495 100644
--- a/cmd/kpod/inspect.go
+++ b/cmd/kpod/inspect.go
@@ -71,6 +71,7 @@ func inspectCmd(c *cli.Context) error {
 	if err != nil {
 		return errors.Wrapf(err, "could not get container server")
 	}
+	defer server.Shutdown()
 	if err = server.Update(); err != nil {
 		return errors.Wrapf(err, "could not update list of containers")
 	}
diff --git a/cmd/kpod/logs.go b/cmd/kpod/logs.go
index 013f7642..995f91cd 100644
--- a/cmd/kpod/logs.go
+++ b/cmd/kpod/logs.go
@@ -69,6 +69,7 @@ func logsCmd(c *cli.Context) error {
 	if err != nil {
 		return errors.Wrapf(err, "could not create container server")
 	}
+	defer server.Shutdown()
 	err = server.Update()
 	if err != nil {
 		return errors.Wrapf(err, "could not update list of containers")
diff --git a/cmd/kpod/main.go b/cmd/kpod/main.go
index 7ee6d854..2aa29845 100644
--- a/cmd/kpod/main.go
+++ b/cmd/kpod/main.go
@@ -50,6 +50,16 @@ func main() {
 		}
 		return nil
 	}
+	app.After = func(*cli.Context) error {
+		// called by Run() when the command handler succeeds
+		shutdownStores()
+		return nil
+	}
+	cli.OsExiter = func(code int) {
+		// called by Run() when the command fails, bypassing After()
+		shutdownStores()
+		os.Exit(code)
+	}
 	app.Flags = []cli.Flag{
 		cli.StringFlag{
 			Name:  "config, c",
@@ -82,6 +92,6 @@ func main() {
 	}
 	if err := app.Run(os.Args); err != nil {
 		logrus.Errorf(err.Error())
-		os.Exit(1)
+		cli.OsExiter(1)
 	}
 }
diff --git a/cmd/kpod/rename.go b/cmd/kpod/rename.go
index 8ef63419..fe1f08d9 100644
--- a/cmd/kpod/rename.go
+++ b/cmd/kpod/rename.go
@@ -32,6 +32,7 @@ func renameCmd(c *cli.Context) error {
 	if err != nil {
 		return errors.Wrapf(err, "could not get container server")
 	}
+	defer server.Shutdown()
 	err = server.Update()
 	if err != nil {
 		return errors.Wrapf(err, "could not update list of containers")
diff --git a/cmd/kpod/stats.go b/cmd/kpod/stats.go
index 10269f71..416acc93 100644
--- a/cmd/kpod/stats.go
+++ b/cmd/kpod/stats.go
@@ -70,6 +70,7 @@ func statsCmd(c *cli.Context) error {
 	if err != nil {
 		return errors.Wrapf(err, "could not create container server")
 	}
+	defer containerServer.Shutdown()
 	err = containerServer.Update()
 	if err != nil {
 		return errors.Wrapf(err, "could not update list of containers")
diff --git a/libkpod/container_server.go b/libkpod/container_server.go
index a495753e..3cf5e90b 100644
--- a/libkpod/container_server.go
+++ b/libkpod/container_server.go
@@ -570,7 +570,10 @@ func (c *ContainerServer) ReleasePodName(name string) {
 // Shutdown attempts to shut down the server's storage cleanly
 func (c *ContainerServer) Shutdown() error {
 	_, err := c.store.Shutdown(false)
-	return err
+	if err != nil && errors.Cause(err) != cstorage.ErrLayerUsedByContainer {
+		return err
+	}
+	return nil
 }
 
 type containerServerState struct {