diff --git a/kyaml/copyutil/copyutil.go b/kyaml/copyutil/copyutil.go
index fa1891110..3b7d01784 100644
--- a/kyaml/copyutil/copyutil.go
+++ b/kyaml/copyutil/copyutil.go
@@ -25,7 +25,7 @@ func CopyDir(src string, dst string) error {
 		// don't copy the .git dir
 		if path != src {
 			rel := strings.TrimPrefix(path, src)
-			if strings.HasPrefix(rel, string(filepath.Separator)+".git") {
+			if IsDotGitFolder(rel) {
 				return nil
 			}
 		}
@@ -67,7 +67,7 @@ func Diff(sourceDir, destDir string) (sets.String, error) {
 		}
 
 		// skip git repo if it exists
-		if strings.Contains(path, ".git") {
+		if IsDotGitFolder(path) {
 			return nil
 		}
 
@@ -86,7 +86,7 @@ func Diff(sourceDir, destDir string) (sets.String, error) {
 		}
 
 		// skip git repo if it exists
-		if strings.Contains(path, ".git") {
+		if IsDotGitFolder(path) {
 			return nil
 		}
 
@@ -129,6 +129,18 @@ func Diff(sourceDir, destDir string) (sets.String, error) {
 	return diff, nil
 }
 
+// IsDotGitFolder checks if the provided path is either the .git folder or
+// a file underneath the .git folder.
+func IsDotGitFolder(path string) bool {
+	cleanPath := filepath.ToSlash(filepath.Clean(path))
+	for _, c := range strings.Split(cleanPath, "/") {
+		if c == ".git" {
+			return true
+		}
+	}
+	return false
+}
+
 // PrettyFileDiff takes the content of two files and returns the pretty diff
 func PrettyFileDiff(s1, s2 string) string {
 	dmp := diffmatchpatch.New()
diff --git a/kyaml/copyutil/copyutil_test.go b/kyaml/copyutil/copyutil_test.go
index 70e73cd1e..8fbb2c23f 100644
--- a/kyaml/copyutil/copyutil_test.go
+++ b/kyaml/copyutil/copyutil_test.go
@@ -154,6 +154,11 @@ func TestDiff_skipGitSrc(t *testing.T) {
 		filepath.Join(s, "a1", "f.yaml"), []byte(`a`), 0600)
 	assert.NoError(t, err)
 
+	// files that just happen to start with .git should not be ignored.
+	err = ioutil.WriteFile(
+		filepath.Join(s, ".gitlab-ci.yml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
 	// git should be ignored
 	err = os.Mkdir(filepath.Join(s, ".git"), 0700)
 	assert.NoError(t, err)
@@ -167,6 +172,10 @@ func TestDiff_skipGitSrc(t *testing.T) {
 		filepath.Join(d, "a1", "f.yaml"), []byte(`a`), 0600)
 	assert.NoError(t, err)
 
+	err = ioutil.WriteFile(
+		filepath.Join(d, ".gitlab-ci.yml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
 	diff, err := Diff(s, d)
 	assert.NoError(t, err)
 	assert.Empty(t, diff.List())
@@ -283,3 +292,99 @@ metadata:
 	assert.Contains(t, PrettyFileDiff(s1, s2), expectedLine1)
 	assert.Contains(t, PrettyFileDiff(s1, s2), expectedLine2)
 }
+
+func TestCopyDir(t *testing.T) {
+	s, err := ioutil.TempDir("", "copyutilsrc")
+	assert.NoError(t, err)
+	v, err := ioutil.TempDir("", "copyutilvalidate")
+	assert.NoError(t, err)
+
+	err = os.Mkdir(filepath.Join(s, "a1"), 0700)
+	assert.NoError(t, err)
+	err = ioutil.WriteFile(
+		filepath.Join(s, "a1", "f.yaml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
+	// files that just happen to start with .git should not be ignored.
+	err = ioutil.WriteFile(
+		filepath.Join(s, ".gitlab-ci.yml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
+	// git should be ignored
+	err = os.Mkdir(filepath.Join(s, ".git"), 0700)
+	assert.NoError(t, err)
+	err = ioutil.WriteFile(
+		filepath.Join(s, ".git", "f.yaml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
+	err = os.Mkdir(filepath.Join(v, "a1"), 0700)
+	assert.NoError(t, err)
+	err = ioutil.WriteFile(
+		filepath.Join(v, "a1", "f.yaml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
+	err = ioutil.WriteFile(
+		filepath.Join(v, ".gitlab-ci.yml"), []byte(`a`), 0600)
+	assert.NoError(t, err)
+
+	d, err := ioutil.TempDir("", "copyutildestination")
+	assert.NoError(t, err)
+
+	err = CopyDir(s, d)
+	assert.NoError(t, err)
+
+	diff, err := Diff(d, v)
+	assert.NoError(t, err)
+	assert.Empty(t, diff.List())
+}
+
+func TestIsDotGitFolder(t *testing.T) {
+	testCases := []struct {
+		name           string
+		path           string
+		isDotGitFolder bool
+	}{
+		{
+			name:           ".git folder",
+			path:           "/foo/bar/.git",
+			isDotGitFolder: true,
+		},
+		{
+			name:           "subfolder of .git folder",
+			path:           "/foo/.git/bar/zoo",
+			isDotGitFolder: true,
+		},
+		{
+			name:           "subfolder of .gitignore folder",
+			path:           "/foo/.gitignore/bar",
+			isDotGitFolder: false,
+		},
+		{
+			name:           ".gitignore file",
+			path:           "foo/bar/.gitignore",
+			isDotGitFolder: false,
+		},
+		{
+			name:           ".gitlab-ci.yml under .git folder",
+			path:           "/foo/.git/bar/.gitignore",
+			isDotGitFolder: true,
+		},
+		{
+			name:           "windows path with .git folder",
+			path:           "c:/foo/.git/bar",
+			isDotGitFolder: true,
+		},
+		{
+			name:           "windows path with .gitignore file",
+			path:           "d:/foo/bar/.gitignore",
+			isDotGitFolder: false,
+		},
+	}
+
+	for i := range testCases {
+		test := testCases[i]
+		t.Run(test.name, func(t *testing.T) {
+			assert.Equal(t, test.isDotGitFolder, IsDotGitFolder(test.path))
+		})
+	}
+}