diff --git a/utils/merkletrie/change.go b/utils/merkletrie/change.go
index 450feb4ba..562ff8902 100644
--- a/utils/merkletrie/change.go
+++ b/utils/merkletrie/change.go
@@ -131,7 +131,9 @@ func (l *Changes) addRecursive(root noder.Path, ctor noderToChangeFn) error {
 	}
 
 	if !root.IsDir() {
-		l.Add(ctor(root))
+		if !root.Skip() {
+			l.Add(ctor(root))
+		}
 		return nil
 	}
 
diff --git a/utils/merkletrie/difftree.go b/utils/merkletrie/difftree.go
index 4ef2d9907..7fc8d02d7 100644
--- a/utils/merkletrie/difftree.go
+++ b/utils/merkletrie/difftree.go
@@ -297,18 +297,16 @@ func DiffTreeContext(ctx context.Context, fromTree, toTree noder.Noder,
 		case noMoreNoders:
 			return ret, nil
 		case onlyFromRemains:
-			if err = ret.AddRecursiveDelete(from); err != nil {
-				return nil, err
+			if !from.Skip() {
+				if err = ret.AddRecursiveDelete(from); err != nil {
+					return nil, err
+				}
 			}
 			if err = ii.nextFrom(); err != nil {
 				return nil, err
 			}
 		case onlyToRemains:
-			if to.Skip() {
-				if err = ret.AddRecursiveDelete(to); err != nil {
-					return nil, err
-				}
-			} else {
+			if !to.Skip() {
 				if err = ret.AddRecursiveInsert(to); err != nil {
 					return nil, err
 				}
@@ -317,26 +315,25 @@ func DiffTreeContext(ctx context.Context, fromTree, toTree noder.Noder,
 				return nil, err
 			}
 		case bothHaveNodes:
-			if from.Skip() {
-				if err = ret.AddRecursiveDelete(from); err != nil {
-					return nil, err
-				}
-				if err := ii.nextBoth(); err != nil {
-					return nil, err
+			var err error
+			switch {
+			case from.Skip():
+				if from.Name() == to.Name() {
+					err = ii.nextBoth()
+				} else {
+					err = ii.nextFrom()
 				}
-				break
-			}
-			if to.Skip() {
-				if err = ret.AddRecursiveDelete(to); err != nil {
-					return nil, err
-				}
-				if err := ii.nextBoth(); err != nil {
-					return nil, err
+			case to.Skip():
+				if from.Name() == to.Name() {
+					err = ii.nextBoth()
+				} else {
+					err = ii.nextTo()
 				}
-				break
+			default:
+				err = diffNodes(&ret, ii)
 			}
 
-			if err = diffNodes(&ret, ii); err != nil {
+			if err != nil {
 				return nil, err
 			}
 		default:
diff --git a/worktree_test.go b/worktree_test.go
index a3dbcfeb3..db2fd7cde 100644
--- a/worktree_test.go
+++ b/worktree_test.go
@@ -1359,7 +1359,24 @@ func (s *WorktreeSuite) TestStatusAfterCheckout(c *C) {
 	status, err := w.Status()
 	c.Assert(err, IsNil)
 	c.Assert(status.IsClean(), Equals, true)
+}
+
+func (s *WorktreeSuite) TestStatusAfterSparseCheckout(c *C) {
+	fs := memfs.New()
+	w := &Worktree{
+		r:          s.Repository,
+		Filesystem: fs,
+	}
 
+	err := w.Checkout(&CheckoutOptions{
+		SparseCheckoutDirectories: []string{"php"},
+		Force:                     true,
+	})
+	c.Assert(err, IsNil)
+
+	status, err := w.Status()
+	c.Assert(err, IsNil)
+	c.Assert(status.IsClean(), Equals, true)
 }
 
 func (s *WorktreeSuite) TestStatusModified(c *C) {