diff --git a/storage/drivers/driver.go b/storage/drivers/driver.go
index 1ca50b6462..510ee700b2 100644
--- a/storage/drivers/driver.go
+++ b/storage/drivers/driver.go
@@ -310,6 +310,11 @@ type DifferOptions struct {
 
 	// UseFsVerity defines whether fs-verity is used
 	UseFsVerity DifferFsVerity
+
+	// StagingDirectory is a writable directory the differ can use for
+	// temporary scratch data.  It must reside on the same filesystem
+	// as the destination directory.
+	StagingDirectory string
 }
 
 // Differ defines the interface for using a custom differ.
diff --git a/storage/drivers/overlay/overlay.go b/storage/drivers/overlay/overlay.go
index 3ade1e7850..cd438e00c2 100644
--- a/storage/drivers/overlay/overlay.go
+++ b/storage/drivers/overlay/overlay.go
@@ -2242,7 +2242,8 @@ func (d *Driver) ApplyDiffWithDiffer(options *graphdriver.ApplyDiffWithDifferOpt
 	logrus.Debugf("Applying differ in %s", applyDir)
 
 	differOptions := graphdriver.DifferOptions{
-		Format: graphdriver.DifferOutputFormatDir,
+		Format:           graphdriver.DifferOutputFormatDir,
+		StagingDirectory: layerDir,
 	}
 	if d.usingComposefs {
 		differOptions.Format = graphdriver.DifferOutputFormatFlat
diff --git a/storage/pkg/chunked/storage_linux.go b/storage/pkg/chunked/storage_linux.go
index ed9a5c7f07..a9f6caecba 100644
--- a/storage/pkg/chunked/storage_linux.go
+++ b/storage/pkg/chunked/storage_linux.go
@@ -36,6 +36,7 @@ import (
 	"go.podman.io/storage/pkg/chunked/internal/minimal"
 	path "go.podman.io/storage/pkg/chunked/internal/path"
 	"go.podman.io/storage/pkg/chunked/toc"
+	"go.podman.io/storage/pkg/fileutils"
 	"go.podman.io/storage/pkg/fsverity"
 	"go.podman.io/storage/pkg/idtools"
 	"go.podman.io/storage/pkg/system"
@@ -625,6 +626,40 @@ func collectIDs(entries []fileMetadata) ([]uint32, []uint32) {
 	return mapToSlice(uids), mapToSlice(gids)
 }
 
+func isReflinkNotSupported(err error) bool {
+	return errors.Is(err, unix.EOPNOTSUPP) ||
+		errors.Is(err, unix.ENOSYS) ||
+		errors.Is(err, unix.EXDEV) ||
+		errors.Is(err, unix.EINVAL)
+}
+
+func createReflink(srcRoot, srcPath, dstDir string) (string, error) {
+	parentDirfd, err := unix.Open(srcRoot, unix.O_RDONLY|unix.O_CLOEXEC, 0)
+	if err != nil {
+		return "", err
+	}
+	defer unix.Close(parentDirfd)
+
+	srcFile, err := openFileUnderRoot(parentDirfd, srcPath, unix.O_RDONLY|unix.O_CLOEXEC, 0)
+	if err != nil {
+		return "", err
+	}
+	defer srcFile.Close()
+
+	dstFile, err := os.CreateTemp(dstDir, "")
+	if err != nil {
+		return "", err
+	}
+	defer dstFile.Close()
+
+	if err := fileutils.Reflink(srcFile, dstFile); err != nil {
+		os.Remove(dstFile.Name())
+		return "", err
+	}
+
+	return filepath.Base(dstFile.Name()), nil
+}
+
 type originFile struct {
 	Root   string
 	Path   string
@@ -1777,6 +1812,29 @@ func (c *chunkedDiffer) ApplyDiff(dest string, options *archive.TarOptions, diff
 
 	wg.Wait()
 
+	// Reflink chunk dedup: when findChunkInOtherLayers locates a chunk
+	// in an existing layer, we cannot use that path directly because
+	// the source layer may be deleted before storeMissingFiles reads
+	// from it.  Instead we reflink (CoW clone) the source file into a
+	// scratch directory so the copy is immune to concurrent deletion.
+	// If the filesystem does not support reflinks we skip chunk dedup
+	// entirely and fetch everything from the network.
+	var chunkRefsDir string
+	if differOpts != nil && differOpts.StagingDirectory != "" {
+		d, err := os.MkdirTemp(differOpts.StagingDirectory, "chunk-refs-")
+		if err != nil {
+			return output, fmt.Errorf("create chunk-refs directory: %w", err)
+		}
+		chunkRefsDir = d
+		defer os.RemoveAll(chunkRefsDir)
+	}
+	// reflinkMap caches reflinks: (source root, source path) → reflinked
+	// filename in chunkRefsDir.  Multiple chunks at different offsets
+	// within the same source file share one reflink.
+	type reflinkKey struct{ root, path string }
+	reflinkMap := make(map[reflinkKey]string)
+	reflinkSupported := chunkRefsDir != ""
+
 	for _, res := range copyResults[:filesToWaitFor] {
 		r := &mergedEntries[res.index]
 
@@ -1820,15 +1878,39 @@ func (c *chunkedDiffer) ApplyDiff(dest string, options *archive.TarOptions, diff
 
 			switch chunk.ChunkType {
 			case minimal.ChunkTypeData:
+				if !reflinkSupported {
+					break
+				}
 				root, path, offset, err := c.layersCache.findChunkInOtherLayers(chunk)
 				if err != nil {
 					return output, err
 				}
-				if offset >= 0 && validateChunkChecksum(chunk, root, path, offset, c.copyBuffer) {
+				if offset < 0 {
+					break
+				}
+				key := reflinkKey{root: root, path: path}
+				refName, ok := reflinkMap[key]
+				if !ok {
+					refName, err = createReflink(root, path, chunkRefsDir)
+					if err != nil {
+						if isReflinkNotSupported(err) {
+							reflinkSupported = false
+							break
+						}
+						// ENOENT is expected: the source layer can
+						// be deleted concurrently.
+						if errors.Is(err, unix.ENOENT) {
+							break
+						}
+						return output, fmt.Errorf("create reflink for %q: %w", path, err)
+					}
+					reflinkMap[key] = refName
+				}
+				if validateChunkChecksum(chunk, chunkRefsDir, refName, offset, c.copyBuffer) {
 					missingPartsSize -= size
 					mp.OriginFile = &originFile{
-						Root:   root,
-						Path:   path,
+						Root:   chunkRefsDir,
+						Path:   refName,
 						Offset: offset,
 					}
 				}
diff --git a/storage/pkg/fileutils/reflink_linux.go b/storage/pkg/fileutils/reflink_linux.go
index 9f5c6c90bb..f0357da159 100644
--- a/storage/pkg/fileutils/reflink_linux.go
+++ b/storage/pkg/fileutils/reflink_linux.go
@@ -7,14 +7,19 @@ import (
 	"golang.org/x/sys/unix"
 )
 
+// Reflink attempts to reflink (CoW clone) the source to the destination fd.
+// Returns an error if the filesystem does not support reflinks.
+func Reflink(src, dst *os.File) error {
+	return unix.IoctlFileClone(int(dst.Fd()), int(src.Fd()))
+}
+
 // ReflinkOrCopy attempts to reflink the source to the destination fd.
 // If reflinking fails or is unsupported, it falls back to io.Copy().
 func ReflinkOrCopy(src, dst *os.File) error {
-	err := unix.IoctlFileClone(int(dst.Fd()), int(src.Fd()))
-	if err == nil {
+	if err := Reflink(src, dst); err == nil {
 		return nil
 	}
 
-	_, err = io.Copy(dst, src)
+	_, err := io.Copy(dst, src)
 	return err
 }
diff --git a/storage/pkg/fileutils/reflink_unsupported.go b/storage/pkg/fileutils/reflink_unsupported.go
index c0a30e670c..2da19d74be 100644
--- a/storage/pkg/fileutils/reflink_unsupported.go
+++ b/storage/pkg/fileutils/reflink_unsupported.go
@@ -3,10 +3,17 @@
 package fileutils
 
 import (
+	"errors"
 	"io"
 	"os"
 )
 
+// Reflink attempts to reflink (CoW clone) the source to the destination fd.
+// Returns an error if the filesystem does not support reflinks.
+func Reflink(src, dst *os.File) error {
+	return errors.ErrUnsupported
+}
+
 // ReflinkOrCopy attempts to reflink the source to the destination fd.
 // If reflinking fails or is unsupported, it falls back to io.Copy().
 func ReflinkOrCopy(src, dst *os.File) error {