diff --git a/pkg/build/paths.go b/pkg/build/paths.go
index 725f6c71c..d247e0031 100644
--- a/pkg/build/paths.go
+++ b/pkg/build/paths.go
@@ -64,6 +64,9 @@ func mutateDirectory(fsys apkfs.FullFS, o *options.Options, mut types.PathMutati
 			if err != nil {
 				return err
 			}
+			if d.Type()&fs.ModeSymlink != 0 {
+				return nil
+			}
 			if err := mutatePermissionsDirect(fsys, path, mut.Permissions, mut.UID, mut.GID); err != nil {
 				return fmt.Errorf("mutating permissions for path %q: %w", path, err)
 			}
@@ -143,7 +146,7 @@ func mutatePaths(fsys apkfs.FullFS, o *options.Options, ic *types.ImageConfigura
 			return fmt.Errorf("mutating path %q: %w", mut.Path, err)
 		}
 
-		if mut.Type != "permissions" {
+		if mut.Type != "permissions" && mut.Type != "symlink" {
 			if err := mutatePermissions(fsys, o, mut); err != nil {
 				return fmt.Errorf("%s mutation on %s: %w", mut.Type, mut.Path, err)
 			}
diff --git a/pkg/build/paths_test.go b/pkg/build/paths_test.go
new file mode 100644
index 000000000..f71baa790
--- /dev/null
+++ b/pkg/build/paths_test.go
@@ -0,0 +1,89 @@
+// Copyright 2026 Chainguard, Inc.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package build
+
+import (
+	"io/fs"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+
+	apkfs "chainguard.dev/apko/pkg/apk/fs"
+	"chainguard.dev/apko/pkg/build/types"
+	"chainguard.dev/apko/pkg/options"
+)
+
+func TestMutatePathsSymlinkAllowsMissingTarget(t *testing.T) {
+	fsys := apkfs.NewMemFS()
+
+	err := mutatePaths(fsys, &options.Default, &types.ImageConfiguration{
+		Paths: []types.PathMutation{{
+			Path:   "/bin/xyz",
+			Type:   "symlink",
+			Source: "/ko-app/abc",
+		}},
+	})
+	require.NoError(t, err)
+
+	target, err := fsys.Readlink("/bin/xyz")
+	require.NoError(t, err)
+	require.Equal(t, "/ko-app/abc", target)
+}
+
+func TestMutatePathsSymlinkDoesNotChangeTargetPermissions(t *testing.T) {
+	fsys := apkfs.NewMemFS()
+	require.NoError(t, fsys.MkdirAll("/var/lib/foo", 0o755))
+
+	err := mutatePaths(fsys, &options.Default, &types.ImageConfiguration{
+		Paths: []types.PathMutation{{
+			Path:   "/foo",
+			Type:   "symlink",
+			Source: "/var/lib/foo",
+		}},
+	})
+	require.NoError(t, err)
+
+	target, err := fsys.Readlink("/foo")
+	require.NoError(t, err)
+	require.Equal(t, "/var/lib/foo", target)
+
+	info, err := fsys.Stat("/var/lib/foo")
+	require.NoError(t, err)
+	require.Equal(t, fs.FileMode(0o755), info.Mode().Perm())
+}
+
+func TestMutateDirectoryRecursiveSkipsSymlinks(t *testing.T) {
+	fsys := apkfs.NewMemFS()
+	require.NoError(t, fsys.MkdirAll("/tree/target", 0o755))
+	require.NoError(t, fsys.Symlink("/missing", "/tree/link"))
+
+	err := mutatePaths(fsys, &options.Default, &types.ImageConfiguration{
+		Paths: []types.PathMutation{{
+			Path:        "/tree",
+			Type:        "directory",
+			Permissions: 0o700,
+			Recursive:   true,
+		}},
+	})
+	require.NoError(t, err)
+
+	target, err := fsys.Readlink("/tree/link")
+	require.NoError(t, err)
+	require.Equal(t, "/missing", target)
+
+	info, err := fsys.Stat("/tree/target")
+	require.NoError(t, err)
+	require.Equal(t, fs.FileMode(0o700), info.Mode().Perm())
+}