diff --git a/cmd/podman/root.go b/cmd/podman/root.go
index a373a3aa18..1ad2cc18be 100644
--- a/cmd/podman/root.go
+++ b/cmd/podman/root.go
@@ -16,6 +16,7 @@ import (
 	"github.com/containers/podman/v5/cmd/podman/registry"
 	"github.com/containers/podman/v5/cmd/podman/validate"
 	"github.com/containers/podman/v5/libpod/define"
+	"github.com/containers/podman/v5/libpod/shutdown"
 	"github.com/containers/podman/v5/pkg/bindings"
 	"github.com/containers/podman/v5/pkg/checkpoint/crutils"
 	"github.com/containers/podman/v5/pkg/domain/entities"
@@ -124,9 +125,11 @@ func Execute() {
 		fmt.Fprintln(os.Stderr, formatError(err))
 	}
 
+	_ = shutdown.Stop()
+
 	if requireCleanup {
 		// The cobra post-run is not being executed in case of
-		// a previous error , so make sure that the engine(s)
+		// a previous error, so make sure that the engine(s)
 		// are correctly shutdown.
 		//
 		// See https://github.com/spf13/cobra/issues/914
diff --git a/libpod/runtime.go b/libpod/runtime.go
index 565a74645e..4c7d06f1f9 100644
--- a/libpod/runtime.go
+++ b/libpod/runtime.go
@@ -210,7 +210,14 @@ func newRuntimeFromConfig(ctx context.Context, conf *config.Config, options ...R
 		}
 	}
 
+	if err := makeRuntime(ctx, runtime); err != nil {
+		return nil, err
+	}
+
 	if err := shutdown.Register("libpod", func(sig os.Signal) error {
+		if runtime.store != nil {
+			_, _ = runtime.store.Shutdown(false)
+		}
 		// For `systemctl stop podman.service` support, exit code should be 0
 		if sig == syscall.SIGTERM {
 			os.Exit(0)
@@ -225,10 +232,6 @@ func newRuntimeFromConfig(ctx context.Context, conf *config.Config, options ...R
 		return nil, fmt.Errorf("starting shutdown signal handler: %w", err)
 	}
 
-	if err := makeRuntime(ctx, runtime); err != nil {
-		return nil, err
-	}
-
 	runtime.config.CheckCgroupsAndAdjustConfig()
 
 	return runtime, nil
diff --git a/libpod/shutdown/handler.go b/libpod/shutdown/handler.go
index 2b30a95768..d7fd5b5323 100644
--- a/libpod/shutdown/handler.go
+++ b/libpod/shutdown/handler.go
@@ -91,6 +91,11 @@ func Stop() error {
 		return nil
 	}
 
+	// if the signal handler is running, wait that it terminates
+	handlerLock.Lock()
+	defer handlerLock.Unlock()
+	// it doesn't need to be in the critical section, but staticcheck complains if
+	// the critical section is empty.
 	cancelChan <- true
 
 	return nil
diff --git a/test/e2e/common_test.go b/test/e2e/common_test.go
index a3c9c72df4..5e0d1df72b 100644
--- a/test/e2e/common_test.go
+++ b/test/e2e/common_test.go
@@ -33,7 +33,6 @@ import (
 	. "github.com/onsi/gomega"
 	. "github.com/onsi/gomega/gexec"
 	"github.com/sirupsen/logrus"
-	"golang.org/x/sys/unix"
 )
 
 var (
@@ -1057,16 +1056,6 @@ func rmAll(podmanBin string, path string) {
 			GinkgoWriter.Printf("%v\n", err)
 		}
 	} else {
-		// When using overlay as root, podman leaves a stray mount behind.
-		// This leak causes remote tests to take a loooooong time, which
-		// then causes Cirrus to time out. Unmount that stray.
-		overlayPath := path + "/root/overlay"
-		if _, err := os.Stat(overlayPath); err == nil {
-			if err = unix.Unmount(overlayPath, unix.MNT_DETACH); err != nil {
-				GinkgoWriter.Printf("Error unmounting %s: %v\n", overlayPath, err)
-			}
-		}
-
 		if err = os.RemoveAll(path); err != nil {
 			GinkgoWriter.Printf("%q\n", err)
 		}
diff --git a/test/e2e/libpod_suite_remote_test.go b/test/e2e/libpod_suite_remote_test.go
index 4c7a7c96f1..44a79eaf36 100644
--- a/test/e2e/libpod_suite_remote_test.go
+++ b/test/e2e/libpod_suite_remote_test.go
@@ -103,7 +103,7 @@ func (p *PodmanTestIntegration) StartRemoteService() {
 }
 
 func (p *PodmanTestIntegration) StopRemoteService() {
-	if err := p.RemoteSession.Kill(); err != nil {
+	if err := p.RemoteSession.Signal(syscall.SIGTERM); err != nil {
 		GinkgoWriter.Printf("unable to clean up service %d, %v\n", p.RemoteSession.Pid, err)
 	}
 	if _, err := p.RemoteSession.Wait(); err != nil {
diff --git a/test/system/001-basic.bats b/test/system/001-basic.bats
index 7c10296290..5cba515e9d 100644
--- a/test/system/001-basic.bats
+++ b/test/system/001-basic.bats
@@ -277,7 +277,7 @@ run_podman --noout system connection ls
     run_podman --log-level=debug run --rm $IMAGE true
     is "$output" ".*Shutting down engines.*"
     run_podman 125 --log-level=debug run dockah://rien.de/rien:latest
-    is "${lines[-1]}" ".*Shutting down engines"
+    is "$output" ".*Shutting down engines.*"
 }
 
 # vim: filetype=sh