diff --git a/deprecated.go b/deprecated.go
index 5fadc27df..beb82b6bf 100644
--- a/deprecated.go
+++ b/deprecated.go
@@ -207,7 +207,6 @@ type LayerStore interface {
 	Mounted(id string) (int, error)
 	ParentOwners(id string) (uids, gids []int, err error)
 	ApplyDiff(to string, diff io.Reader) (int64, error)
-	ApplyDiffWithDiffer(to string, options *drivers.ApplyDiffOpts, differ drivers.Differ) (*drivers.DriverWithDifferOutput, error)
 	DifferTarget(id string) (string, error)
 	LoadLocked() error
 	PutAdditionalLayer(id string, parentLayer *Layer, names []string, aLayer drivers.AdditionalLayer) (layer *Layer, err error)
diff --git a/pkg/chunked/storage_linux.go b/pkg/chunked/storage_linux.go
index bbacff998..75f3634da 100644
--- a/pkg/chunked/storage_linux.go
+++ b/pkg/chunked/storage_linux.go
@@ -199,7 +199,7 @@ func (c *chunkedDiffer) Close() error {
 	return nil
 }
 
-// GetDiffer returns a differ than can be used with ApplyDiffWithDiffer.
+// GetDiffer returns a differ than can be used with [Store.PrepareStagedLayer].
 // If it returns an error that matches ErrFallbackToOrdinaryLayerDownload, the caller can
 // retry the operation with a different method.
 func GetDiffer(ctx context.Context, store storage.Store, blobDigest digest.Digest, blobSize int64, annotations map[string]string, iss ImageSourceSeekable) (graphdriver.Differ, error) {
diff --git a/pkg/chunked/storage_unsupported.go b/pkg/chunked/storage_unsupported.go
index fe3d36c76..daed1359e 100644
--- a/pkg/chunked/storage_unsupported.go
+++ b/pkg/chunked/storage_unsupported.go
@@ -11,7 +11,7 @@ import (
 	digest "github.com/opencontainers/go-digest"
 )
 
-// GetDiffer returns a differ than can be used with ApplyDiffWithDiffer.
+// GetDiffer returns a differ than can be used with [Store.PrepareStagedLayer].
 func GetDiffer(ctx context.Context, store storage.Store, blobDigest digest.Digest, blobSize int64, annotations map[string]string, iss ImageSourceSeekable) (graphdriver.Differ, error) {
 	return nil, newErrFallbackToOrdinaryLayerDownload(errors.New("format not supported on this system"))
 }
diff --git a/store.go b/store.go
index 869b0c516..e525ff590 100644
--- a/store.go
+++ b/store.go
@@ -362,12 +362,6 @@ type Store interface {
 	//   }
 	ApplyDiff(to string, diff io.Reader) (int64, error)
 
-	// ApplyDiffWithDiffer applies a diff to a layer.
-	// It is the caller responsibility to clean the staging directory if it is not
-	// successfully applied with ApplyStagedLayer.
-	// Deprecated: Use PrepareStagedLayer instead.  ApplyDiffWithDiffer is going to be removed in a future release
-	ApplyDiffWithDiffer(to string, options *drivers.ApplyDiffWithDifferOpts, differ drivers.Differ) (*drivers.DriverWithDifferOutput, error)
-
 	// PrepareStagedLayer applies a diff to a layer.
 	// It is the caller responsibility to clean the staging directory if it is not
 	// successfully applied with ApplyStagedLayer.
@@ -3177,13 +3171,6 @@ func (s *store) PrepareStagedLayer(options *drivers.ApplyDiffWithDifferOpts, dif
 	return rlstore.applyDiffWithDifferNoLock(options, differ)
 }
 
-func (s *store) ApplyDiffWithDiffer(to string, options *drivers.ApplyDiffWithDifferOpts, differ drivers.Differ) (*drivers.DriverWithDifferOutput, error) {
-	if to != "" {
-		return nil, fmt.Errorf("ApplyDiffWithDiffer does not support non-empty 'layer' parameter")
-	}
-	return s.PrepareStagedLayer(options, differ)
-}
-
 func (s *store) DifferTarget(id string) (string, error) {
 	return writeToLayerStore(s, func(rlstore rwLayerStore) (string, error) {
 		if rlstore.Exists(id) {