diff --git a/common/pkg/secrets/secrets.go b/common/pkg/secrets/secrets.go
index 1edf766168..3d3a47d407 100644
--- a/common/pkg/secrets/secrets.go
+++ b/common/pkg/secrets/secrets.go
@@ -199,6 +199,26 @@ func (s *SecretsManager) Store(name string, data []byte, driverType string, opti
 		if options.IgnoreIfExists {
 			return secr.ID, nil
 		}
+
+		if options.Replace {
+			// We must call Delete using whatever driver the secret was created with,
+			// which is not necessarily driver where the new value will go
+			prevDriver, err := getDriver(secr.Driver, secr.DriverOptions)
+			if err != nil {
+				return "", err
+			}
+			err = prevDriver.Delete(secr.ID)
+			if err != nil {
+				if !errors.Is(err, define.ErrNoSuchSecret) {
+					return "", fmt.Errorf("deleting driver secret %s: %w", secr.ID, err)
+				}
+			} else {
+				if err := s.delete(secr.ID); err != nil && !errors.Is(err, define.ErrNoSuchSecret) {
+					return "", fmt.Errorf("deleting secret %s: %w", secr.ID, err)
+				}
+			}
+		}
+
 		secr.UpdatedAt = time.Now()
 	} else {
 		secr = new(Secret)
@@ -227,19 +247,6 @@ func (s *SecretsManager) Store(name string, data []byte, driverType string, opti
 		return "", err
 	}
 
-	if options.Replace {
-		err := driver.Delete(secr.ID)
-		if err != nil {
-			if !errors.Is(err, define.ErrNoSuchSecret) {
-				return "", fmt.Errorf("deleting driver secret %s: %w", secr.ID, err)
-			}
-		} else {
-			if err := s.delete(secr.ID); err != nil && !errors.Is(err, define.ErrNoSuchSecret) {
-				return "", fmt.Errorf("deleting secret %s: %w", secr.ID, err)
-			}
-		}
-	}
-
 	secr.ID, err = s.newID()
 	if err != nil {
 		return "", err
diff --git a/common/pkg/secrets/secrets_test.go b/common/pkg/secrets/secrets_test.go
index 2f720da1dc..81030b759a 100644
--- a/common/pkg/secrets/secrets_test.go
+++ b/common/pkg/secrets/secrets_test.go
@@ -2,9 +2,13 @@ package secrets
 
 import (
 	"bytes"
+	"fmt"
 	"testing"
 
 	"github.com/stretchr/testify/require"
+
+	"go.podman.io/common/pkg/secrets/filedriver"
+	"go.podman.io/common/pkg/secrets/shelldriver"
 )
 
 var drivertype = "file"
@@ -300,3 +304,90 @@ func TestSecretList(t *testing.T) {
 	require.NoError(t, err)
 	require.Len(t, allSecrets, 2)
 }
+
+// Creating a new secret with Replace=true should not remove other existing secrets.
+func TestReplaceNewSecretDoesNotDeleteOthers(t *testing.T) {
+	manager, _ := setup(t)
+
+	// file driver storage
+	pathFile := t.TempDir()
+	fileOpts := StoreOptions{DriverOpts: map[string]string{"path": pathFile}}
+
+	// shell driver storage (different directory)
+	shellBase := t.TempDir()
+	shellOptsMap := map[string]string{
+		"store":  fmt.Sprintf("cat - > %s/${SECRET_ID}", shellBase),
+		"lookup": fmt.Sprintf("cat %s/${SECRET_ID}", shellBase),
+		"delete": "true", // emulate a non-zero exit code
+		"list":   "true",
+	}
+	shellOpts := StoreOptions{DriverOpts: shellOptsMap, Replace: true}
+
+	// Store first secret using file driver
+	id1, err := manager.Store("test1", []byte("data1"), "file", fileOpts)
+	require.NoError(t, err)
+	require.NotEmpty(t, id1)
+
+	// Store a new secret using shell driver and Replace=true (should not affect test1)
+	id2, err := manager.Store("test2", []byte("data2"), "shell", shellOpts)
+	require.NoError(t, err)
+	require.NotEmpty(t, id2)
+
+	// Both secrets should exist in the manager
+	all, err := manager.List()
+	require.NoError(t, err)
+	require.Len(t, all, 2)
+
+	// Verify file driver data still contains id1
+	fd, err := filedriver.NewDriver(pathFile)
+	require.NoError(t, err)
+	d1, err := fd.Lookup(id1)
+	require.NoError(t, err)
+	require.Equal(t, []byte("data1"), d1)
+
+	// Verify shell storage contains id2
+	sd, err := shelldriver.NewDriver(shellOptsMap)
+	require.NoError(t, err)
+	d2, err := sd.Lookup(id2)
+	require.NoError(t, err)
+	require.Equal(t, []byte("data2"), d2)
+}
+
+func TestReplaceUsesOriginalDriverToDelete(t *testing.T) {
+	manager, _ := setup(t)
+
+	// Two separate filedriver storage roots
+	path1 := t.TempDir()
+	path2 := t.TempDir()
+
+	// Store secret initially in path1
+	storeOpts1 := StoreOptions{DriverOpts: map[string]string{"path": path1}}
+	id1, err := manager.Store("mysecret", []byte("orig"), "file", storeOpts1)
+	require.NoError(t, err)
+	require.NotEmpty(t, id1)
+
+	// Ensure the secret entry exists in path1 data file
+	fd1, err := filedriver.NewDriver(path1)
+	require.NoError(t, err)
+	dOrig, err := fd1.Lookup(id1)
+	require.NoError(t, err)
+	require.Equal(t, []byte("orig"), dOrig)
+
+	// Replace the secret using a different driver storage path (path2)
+	storeOpts2 := StoreOptions{DriverOpts: map[string]string{"path": path2}, Replace: true}
+	id2, err := manager.Store("mysecret", []byte("new"), "file", storeOpts2)
+	require.NoError(t, err)
+	require.NotEmpty(t, id2)
+	require.NotEqual(t, id1, id2)
+
+	// Old id should no longer exist in path1 (deleted via previous driver)
+	_, err = fd1.Lookup(id1)
+	require.Error(t, err, "old secret id should no longer exist in path1")
+
+	// New id should exist in path2
+	fd2, err := filedriver.NewDriver(path2)
+	require.NoError(t, err)
+	dNew, err := fd2.Lookup(id2)
+	require.NoError(t, err)
+	require.Equal(t, []byte("new"), dNew)
+}