diff --git a/Makefile b/Makefile
index 360ff91d4..a58e935bc 100644
--- a/Makefile
+++ b/Makefile
@@ -266,17 +266,17 @@ simple-tests: unit-tests # Compatibility target.
 INTEGRATION_TARGETS := //test/image:image_test //test/e2e:integration_test
 
 docker-tests: load-basic $(RUNTIME_BIN)
-	@$(call install_runtime,$(RUNTIME),) # Clear flags.
+	@$(call install_runtime,$(RUNTIME),--overlay2=none)
 	@$(call install_runtime,$(RUNTIME)-fdlimit,--fdlimit=2000) # Used by TestRlimitNoFile.
 	@$(call install_runtime,$(RUNTIME)-dcache,--fdlimit=2000 --dcache=100) # Used by TestDentryCacheLimit.
 	@$(call install_runtime,$(RUNTIME)-host-uds,--host-uds=all) # Used by TestHostSocketConnect.
 	@$(call install_runtime,$(RUNTIME)-overlay,--overlay2=all:self) # Used by TestOverlay*.
+	@$(call install_runtime,$(RUNTIME)-no-overlay,--overlay2=none) # Used by TestCheckpointRestore.
 	@$(call test_runtime,$(RUNTIME),$(INTEGRATION_TARGETS) //test/e2e:integration_runtime_test)
 .PHONY: docker-tests
 
-# TODO(b/241832602): Run overlay tests with host filestore option after S/R support is added.
 overlay-tests: load-basic $(RUNTIME_BIN)
-	@$(call install_runtime,$(RUNTIME),--overlay2=all:memory)
+	@$(call install_runtime,$(RUNTIME),--overlay2=all:dir=/tmp)
 	@$(call test_runtime,$(RUNTIME),--test_env=TEST_OVERLAY=true $(INTEGRATION_TARGETS))
 .PHONY: overlay-tests
 
diff --git a/pkg/sentry/fsimpl/tmpfs/save_restore.go b/pkg/sentry/fsimpl/tmpfs/save_restore.go
index a540e8915..d08975d82 100644
--- a/pkg/sentry/fsimpl/tmpfs/save_restore.go
+++ b/pkg/sentry/fsimpl/tmpfs/save_restore.go
@@ -17,7 +17,7 @@ package tmpfs
 // afterLoad is called by stateify.
 func (fs *filesystem) afterLoad() {
 	if fs.privateMF {
-		// TODO(b/241832602): Add S/R support.
+		// TODO(b/271612187): Add S/R support.
 		panic("S/R not supported for private memory files")
 	}
 	fs.mf = fs.mfp.MemoryFile()
diff --git a/pkg/test/testutil/testutil.go b/pkg/test/testutil/testutil.go
index bb8b9e823..db24a0482 100644
--- a/pkg/test/testutil/testutil.go
+++ b/pkg/test/testutil/testutil.go
@@ -467,6 +467,20 @@ func WaitForHTTP(ip string, port int, timeout time.Duration) error {
 	return Poll(cb, timeout)
 }
 
+// HTTPRequestSucceeds sends a request to a given url and checks that the status is OK.
+func HTTPRequestSucceeds(client http.Client, server string, port int) error {
+	url := fmt.Sprintf("http://%s:%d", server, port)
+	// Ensure that content is being served.
+	resp, err := client.Get(url)
+	if err != nil {
+		return fmt.Errorf("error reaching http server: %v", err)
+	}
+	if want := http.StatusOK; resp.StatusCode != want {
+		return fmt.Errorf("wrong response code, got: %d, want: %d", resp.StatusCode, want)
+	}
+	return nil
+}
+
 // Reaper reaps child processes.
 type Reaper struct {
 	// mu protects ch, which will be nil if the reaper is not running.
diff --git a/runsc/cmd/do.go b/runsc/cmd/do.go
index f6ef57456..8292f9040 100644
--- a/runsc/cmd/do.go
+++ b/runsc/cmd/do.go
@@ -146,9 +146,12 @@ func (c *Do) Execute(_ context.Context, f *flag.FlagSet, args ...any) subcommand
 		return util.Errorf("Error to retrieve hostname: %v", err)
 	}
 
-	// If c.overlay is set, then forcefully enable overlay.
-	if overlay2 := conf.GetOverlay2(); c.overlay && !overlay2.Enabled() {
-		conf.Overlay = true
+	// If c.overlay is set, then enable overlay.
+	conf.Overlay = false // conf.Overlay is deprecated.
+	if c.overlay {
+		conf.Overlay2 = config.Overlay2{RootMount: true, SubMounts: true, Medium: "memory"}
+	} else {
+		conf.Overlay2 = config.Overlay2{RootMount: false, SubMounts: false, Medium: ""}
 	}
 	absRoot, err := resolvePath(c.root)
 	if err != nil {
diff --git a/runsc/config/config.go b/runsc/config/config.go
index 292e4d040..948b7675c 100644
--- a/runsc/config/config.go
+++ b/runsc/config/config.go
@@ -322,7 +322,7 @@ func (c *Config) validate() error {
 		return fmt.Errorf("overlay flag has been replaced with overlay2 flag")
 	}
 	if overlay2 := c.GetOverlay2(); c.FileAccess == FileAccessShared && overlay2.Enabled() {
-		return fmt.Errorf("overlay flag is incompatible with shared file access")
+		return fmt.Errorf("overlay flag is incompatible with shared file access for rootfs")
 	}
 	if c.NumNetworkChannels <= 0 {
 		return fmt.Errorf("num_network_channels must be > 0, got: %d", c.NumNetworkChannels)
@@ -705,7 +705,9 @@ func defaultOverlay2() *Overlay2 {
 // Set implements flag.Value.
 func (o *Overlay2) Set(v string) error {
 	if v == "none" {
-		// Defaults are correct.
+		o.RootMount = false
+		o.SubMounts = false
+		o.Medium = ""
 		return nil
 	}
 	vs := strings.Split(v, ":")
diff --git a/runsc/config/config_test.go b/runsc/config/config_test.go
index 97bd431ab..679da8c62 100644
--- a/runsc/config/config_test.go
+++ b/runsc/config/config_test.go
@@ -252,7 +252,7 @@ func TestValidationFail(t *testing.T) {
 			name: "shared+overlay",
 			flags: map[string]string{
 				"file-access": "shared",
-				"overlay":     "true",
+				"overlay2":    "root:self",
 			},
 			error: "overlay flag is incompatible",
 		},
diff --git a/runsc/container/container_test.go b/runsc/container/container_test.go
index 7591dfe89..f940ca272 100644
--- a/runsc/container/container_test.go
+++ b/runsc/container/container_test.go
@@ -408,6 +408,7 @@ func configs(t *testing.T, noOverlay bool) map[string]*config.Config {
 	cs := make(map[string]*config.Config)
 	for _, p := range ps {
 		c := testutil.TestConfig(t)
+		c.Overlay2 = config.Overlay2{RootMount: false, SubMounts: false, Medium: ""}
 		c.Platform = p
 		cs[p] = c
 	}
@@ -417,7 +418,7 @@ func configs(t *testing.T, noOverlay bool) map[string]*config.Config {
 		for _, p := range ps {
 			c := testutil.TestConfig(t)
 			c.Platform = p
-			c.Overlay = true
+			c.Overlay2 = config.Overlay2{RootMount: true, SubMounts: true, Medium: "memory"}
 			cs[p+"-overlay"] = c
 		}
 	}
@@ -616,7 +617,8 @@ func TestExePath(t *testing.T) {
 		"default": testutil.TestConfig(t),
 		"overlay": testutil.TestConfig(t),
 	}
-	configs["overlay"].Overlay = true
+	configs["default"].Overlay2 = config.Overlay2{RootMount: false, SubMounts: false, Medium: ""}
+	configs["overlay"].Overlay2 = config.Overlay2{RootMount: true, SubMounts: true, Medium: "memory"}
 
 	for name, conf := range configs {
 		t.Run(name, func(t *testing.T) {
diff --git a/runsc/container/multi_container_test.go b/runsc/container/multi_container_test.go
index 4fa717d5f..2c9be0efa 100644
--- a/runsc/container/multi_container_test.go
+++ b/runsc/container/multi_container_test.go
@@ -1086,7 +1086,7 @@ func TestMultiContainerDifferentFilesystems(t *testing.T) {
 
 	// Make sure overlay is enabled, and none of the root filesystems are
 	// read-only, otherwise we won't be able to create the file.
-	conf.Overlay = true
+	conf.Overlay2 = config.Overlay2{RootMount: true, SubMounts: true, Medium: "memory"}
 	specs, ids := createSpecs(cmdRoot, cmd, cmd)
 	for _, s := range specs {
 		s.Root.Readonly = false
diff --git a/runsc/container/shared_volume_test.go b/runsc/container/shared_volume_test.go
index 8d8402886..7d274de38 100644
--- a/runsc/container/shared_volume_test.go
+++ b/runsc/container/shared_volume_test.go
@@ -33,6 +33,7 @@ import (
 // into and out of the sandbox.
 func TestSharedVolume(t *testing.T) {
 	conf := testutil.TestConfig(t)
+	conf.Overlay2 = config.Overlay2{RootMount: false, SubMounts: false, Medium: ""}
 	conf.FileAccess = config.FileAccessShared
 
 	// Main process just sleeps. We will use "exec" to probe the state of
@@ -145,11 +146,6 @@ func TestSharedVolume(t *testing.T) {
 		t.Errorf("stat %q got error %v, wanted nil", filename, err)
 	}
 
-	// File should exist outside the sandbox.
-	if _, err := os.Stat(filename); err != nil {
-		t.Errorf("stat %q got error %v, wanted nil", filename, err)
-	}
-
 	// Delete the file from within the sandbox.
 	argsRemove := &control.ExecArgs{
 		Filename: "/bin/rm",
@@ -186,6 +182,7 @@ func checkFile(conf *config.Config, c *Container, filename string, want []byte)
 // is reflected inside.
 func TestSharedVolumeFile(t *testing.T) {
 	conf := testutil.TestConfig(t)
+	conf.Overlay2 = config.Overlay2{RootMount: false, SubMounts: false, Medium: ""}
 	conf.FileAccess = config.FileAccessShared
 
 	// Main process just sleeps. We will use "exec" to probe the state of
diff --git a/test/e2e/integration_runtime_test.go b/test/e2e/integration_runtime_test.go
index 0010197da..b101a4af7 100644
--- a/test/e2e/integration_runtime_test.go
+++ b/test/e2e/integration_runtime_test.go
@@ -27,6 +27,7 @@ import (
 	"fmt"
 	"io/ioutil"
 	"net"
+	"net/http"
 	"os"
 	"path/filepath"
 	"strconv"
@@ -213,3 +214,56 @@ func TestOverlayRootfsWhiteout(t *testing.T) {
 		t.Errorf("root directory contains a file/directory whose name contains %q: output = %q", boot.SelfOverlayFilestorePrefix, got)
 	}
 }
+
+// TODO(b/271612187): Once S/R support is added for file-backed overlays, move
+// this test to integration_test.go so it can run with the default runsc
+// configuration which uses file-backed overlay.
+func TestCheckpointRestore(t *testing.T) {
+	if !testutil.IsCheckpointSupported() {
+		t.Skip("Pause/resume is not supported.")
+	}
+	dockerutil.EnsureDockerExperimentalEnabled()
+
+	ctx := context.Background()
+	d := dockerutil.MakeContainerWithRuntime(ctx, t, "-no-overlay")
+	defer d.CleanUp(ctx)
+
+	// Start the container.
+	port := 8080
+	if err := d.Spawn(ctx, dockerutil.RunOpts{
+		Image: "basic/python",
+		Ports: []int{port}, // See Dockerfile.
+	}); err != nil {
+		t.Fatalf("docker run failed: %v", err)
+	}
+
+	// Create a snapshot.
+	if err := d.Checkpoint(ctx, "test"); err != nil {
+		t.Fatalf("docker checkpoint failed: %v", err)
+	}
+	if err := d.WaitTimeout(ctx, defaultWait); err != nil {
+		t.Fatalf("wait failed: %v", err)
+	}
+
+	// TODO(b/143498576): Remove Poll after github.com/moby/moby/issues/38963 is fixed.
+	if err := testutil.Poll(func() error { return d.Restore(ctx, "test") }, defaultWait); err != nil {
+		t.Fatalf("docker restore failed: %v", err)
+	}
+
+	// Find container IP address.
+	ip, err := d.FindIP(ctx, false)
+	if err != nil {
+		t.Fatalf("docker.FindIP failed: %v", err)
+	}
+
+	// Wait until it's up and running.
+	if err := testutil.WaitForHTTP(ip.String(), port, defaultWait); err != nil {
+		t.Fatalf("WaitForHTTP() timeout: %v", err)
+	}
+
+	// Check if container is working again.
+	client := http.Client{Timeout: defaultWait}
+	if err := testutil.HTTPRequestSucceeds(client, ip.String(), port); err != nil {
+		t.Error("http request failed:", err)
+	}
+}
diff --git a/test/e2e/integration_test.go b/test/e2e/integration_test.go
index d506f467b..f0bb18e86 100644
--- a/test/e2e/integration_test.go
+++ b/test/e2e/integration_test.go
@@ -56,20 +56,6 @@ func TestMain(m *testing.M) {
 	os.Exit(m.Run())
 }
 
-// httpRequestSucceeds sends a request to a given url and checks that the status is OK.
-func httpRequestSucceeds(client http.Client, server string, port int) error {
-	url := fmt.Sprintf("http://%s:%d", server, port)
-	// Ensure that content is being served.
-	resp, err := client.Get(url)
-	if err != nil {
-		return fmt.Errorf("error reaching http server: %v", err)
-	}
-	if want := http.StatusOK; resp.StatusCode != want {
-		return fmt.Errorf("wrong response code, got: %d, want: %d", resp.StatusCode, want)
-	}
-	return nil
-}
-
 // TestLifeCycle tests a basic Create/Start/Stop docker container life cycle.
 func TestLifeCycle(t *testing.T) {
 	ctx := context.Background()
@@ -96,7 +82,7 @@ func TestLifeCycle(t *testing.T) {
 		t.Fatalf("WaitForHTTP() timeout: %v", err)
 	}
 	client := http.Client{Timeout: defaultWait}
-	if err := httpRequestSucceeds(client, ip.String(), port); err != nil {
+	if err := testutil.HTTPRequestSucceeds(client, ip.String(), port); err != nil {
 		t.Errorf("http request failed: %v", err)
 	}
 
@@ -139,7 +125,7 @@ func TestPauseResume(t *testing.T) {
 
 	// Check that container is working.
 	client := http.Client{Timeout: defaultWait}
-	if err := httpRequestSucceeds(client, ip.String(), port); err != nil {
+	if err := testutil.HTTPRequestSucceeds(client, ip.String(), port); err != nil {
 		t.Error("http request failed:", err)
 	}
 
@@ -171,57 +157,7 @@ func TestPauseResume(t *testing.T) {
 
 	// Check if container is working again.
 	client = http.Client{Timeout: defaultWait}
-	if err := httpRequestSucceeds(client, ip.String(), port); err != nil {
-		t.Error("http request failed:", err)
-	}
-}
-
-func TestCheckpointRestore(t *testing.T) {
-	if !testutil.IsCheckpointSupported() {
-		t.Skip("Pause/resume is not supported.")
-	}
-	dockerutil.EnsureDockerExperimentalEnabled()
-
-	ctx := context.Background()
-	d := dockerutil.MakeContainer(ctx, t)
-	defer d.CleanUp(ctx)
-
-	// Start the container.
-	port := 8080
-	if err := d.Spawn(ctx, dockerutil.RunOpts{
-		Image: "basic/python",
-		Ports: []int{port}, // See Dockerfile.
-	}); err != nil {
-		t.Fatalf("docker run failed: %v", err)
-	}
-
-	// Create a snapshot.
-	if err := d.Checkpoint(ctx, "test"); err != nil {
-		t.Fatalf("docker checkpoint failed: %v", err)
-	}
-	if err := d.WaitTimeout(ctx, defaultWait); err != nil {
-		t.Fatalf("wait failed: %v", err)
-	}
-
-	// TODO(b/143498576): Remove Poll after github.com/moby/moby/issues/38963 is fixed.
-	if err := testutil.Poll(func() error { return d.Restore(ctx, "test") }, defaultWait); err != nil {
-		t.Fatalf("docker restore failed: %v", err)
-	}
-
-	// Find container IP address.
-	ip, err := d.FindIP(ctx, false)
-	if err != nil {
-		t.Fatalf("docker.FindIP failed: %v", err)
-	}
-
-	// Wait until it's up and running.
-	if err := testutil.WaitForHTTP(ip.String(), port, defaultWait); err != nil {
-		t.Fatalf("WaitForHTTP() timeout: %v", err)
-	}
-
-	// Check if container is working again.
-	client := http.Client{Timeout: defaultWait}
-	if err := httpRequestSucceeds(client, ip.String(), port); err != nil {
+	if err := testutil.HTTPRequestSucceeds(client, ip.String(), port); err != nil {
 		t.Error("http request failed:", err)
 	}
 }
diff --git a/test/runner/main.go b/test/runner/main.go
index 63592841f..c017499dd 100644
--- a/test/runner/main.go
+++ b/test/runner/main.go
@@ -238,6 +238,8 @@ func runRunsc(tc *gtest.TestCase, spec *specs.Spec) error {
 	}
 	if *overlay {
 		args = append(args, "-overlay2=all:dir=/tmp")
+	} else {
+		args = append(args, "-overlay2=none")
 	}
 	if *debug {
 		args = append(args, "-debug", "-log-packets=true")
diff --git a/test/runtimes/exclude/python3.10.2.csv b/test/runtimes/exclude/python3.10.2.csv
index f665b22c7..6ca462a12 100644
--- a/test/runtimes/exclude/python3.10.2.csv
+++ b/test/runtimes/exclude/python3.10.2.csv
@@ -8,3 +8,4 @@ test_readline,b/162980389,TestReadline hangs forever
 test_resource,b/76174079,
 test_signal,,Flaky - signal: alarm clock
 test_socket,,Broken test
+test_os,b/271473320,TestScandir.test_attributes fails with overlay