diff --git a/pkg/manifests/configaware.go b/pkg/manifests/configaware.go
index 161899bad..a6242932f 100644
--- a/pkg/manifests/configaware.go
+++ b/pkg/manifests/configaware.go
@@ -81,6 +81,10 @@ func splitConfigFilesAndRawManifestPaths(baseDir string, paths []string) ([]*Con
 		if err != nil {
 			return nil, nil, fmt.Errorf("cannot parse config file: %s", err)
 		}
+		if cf.IsJustFiles() {
+			rawManifestPaths = append(rawManifestPaths, path)
+			continue
+		}
 		configFiles = append(configFiles, cf)
 	}
 
diff --git a/pkg/manifests/configaware_test.go b/pkg/manifests/configaware_test.go
index c33c53d9c..892b1a9df 100644
--- a/pkg/manifests/configaware_test.go
+++ b/pkg/manifests/configaware_test.go
@@ -384,3 +384,30 @@ func TestDuplicateInGenerators(t *testing.T) {
 	assert.Error(t, err)
 	assert.Contains(t, err.Error(), "duplicate")
 }
+
+func TestJustFiles(t *testing.T) {
+	// +-- config
+	//   +-- .flux.yaml (patchUpdated)
+	//   +-- rawfiles
+	//     +-- .flux.yaml (files)
+	//     +-- manifest.yaml
+
+	manifestyaml := `
+apiVersion: v1
+kind: Namespace
+metadata:
+  name: foo-ns
+`
+
+	config, baseDir, cleanup := setup(t, []string{filepath.Join("config", "rawfiles")},
+		config{path: "config", fluxyaml: patchUpdatedEchoConfigFile},
+		config{path: filepath.Join("config", "rawfiles"), fluxyaml: "version: 1\nfiles: {}\n"},
+	)
+	defer cleanup()
+
+	assert.NoError(t, ioutil.WriteFile(filepath.Join(baseDir, "config", "rawfiles", "manifest.yaml"), []byte(manifestyaml), 0600))
+
+	res, err := config.GetAllResourcesByID(context.Background())
+	assert.NoError(t, err)
+	assert.Contains(t, res, "default:namespace/foo-ns")
+}
diff --git a/pkg/manifests/configfile.go b/pkg/manifests/configfile.go
index dea0a3496..3193ef1ae 100644
--- a/pkg/manifests/configfile.go
+++ b/pkg/manifests/configfile.go
@@ -155,6 +155,15 @@ type PatchUpdated struct {
 type Files struct {
 }
 
+// IsJustFiles returns true if the config file indicates that the
+// directory should be treated as containing YAML files (i.e., should
+// act as though there was no config file in operation). This can be
+// used to reset the directive given by a .flux.yaml higher in the
+// directory structure.
+func (cf *ConfigFile) IsJustFiles() bool {
+	return cf.Files != nil
+}
+
 func ParseConfigFile(fileBytes []byte, result *ConfigFile) error {
 	// The file contents are unmarshaled into a map so that we will
 	// see any extraneous fields. This is important, for example, for
diff --git a/pkg/manifests/configfile_test.go b/pkg/manifests/configfile_test.go
index 933bef960..d0607370c 100644
--- a/pkg/manifests/configfile_test.go
+++ b/pkg/manifests/configfile_test.go
@@ -82,6 +82,19 @@ files: {}
 	}
 }
 
+const justFilesConfigFile = `
+version: 1
+files: {}
+`
+
+func TestJustFileDirective(t *testing.T) {
+	var cf ConfigFile
+	err := ParseConfigFile([]byte(justFilesConfigFile), &cf)
+	assert.NoError(t, err)
+
+	assert.True(t, cf.IsJustFiles())
+}
+
 const patchUpdatedConfigFile = `---
 version: 1
 patchUpdated:
@@ -96,6 +109,7 @@ func TestParsePatchUpdatedConfigFile(t *testing.T) {
 	if err := ParseConfigFile([]byte(patchUpdatedConfigFile), &cf); err != nil {
 		t.Fatal(err)
 	}
+	assert.False(t, cf.IsJustFiles())
 	assert.NotNil(t, cf.PatchUpdated)
 	assert.Nil(t, cf.CommandUpdated)
 	assert.Equal(t, 1, cf.Version)
@@ -126,6 +140,7 @@ func TestParseCmdUpdatedConfigFile(t *testing.T) {
 	if err := ParseConfigFile([]byte(echoCmdUpdatedConfigFile), &cf); err != nil {
 		t.Fatal(err)
 	}
+	assert.False(t, cf.IsJustFiles())
 	assert.NotNil(t, cf.CommandUpdated)
 	assert.Nil(t, cf.PatchUpdated)
 	assert.Equal(t, 1, cf.Version)
diff --git a/pkg/manifests/rawfiles.go b/pkg/manifests/rawfiles.go
index 9945ba736..efd2b022b 100644
--- a/pkg/manifests/rawfiles.go
+++ b/pkg/manifests/rawfiles.go
@@ -17,6 +17,8 @@ type rawFiles struct {
 	manifests Manifests
 }
 
+// NewRawFiles constructs a `Store` that assumes the provided
+// directories contain plain YAML files
 func NewRawFiles(baseDir string, paths []string, manifests Manifests) *rawFiles {
 	return &rawFiles{
 		baseDir:   baseDir,