diff --git a/pkg/skaffold/schema/versions.go b/pkg/skaffold/schema/versions.go
index 72ca24fc688..cf4a0c6230f 100644
--- a/pkg/skaffold/schema/versions.go
+++ b/pkg/skaffold/schema/versions.go
@@ -151,7 +151,7 @@ func ParseConfig(filename string) ([]util.VersionedConfig, error) {
 	if err != nil {
 		return nil, fmt.Errorf("read skaffold config: %w", err)
 	}
-	factory, err := configFactoryFromAPIVersion(buf)
+	factories, err := configFactoryFromAPIVersion(buf)
 	if err != nil {
 		return nil, err
 	}
@@ -159,7 +159,7 @@ func ParseConfig(filename string) ([]util.VersionedConfig, error) {
 	if err != nil {
 		return nil, fmt.Errorf("unable to re-marshal YAML without dotted keys: %w", err)
 	}
-	return parseConfig(buf, factory)
+	return parseConfig(buf, factories)
 }
 
 // ParseConfigAndUpgrade reads a configuration file and upgrades it to a given version.
@@ -211,14 +211,14 @@ func ParseConfigAndUpgrade(filename, toVersion string) ([]util.VersionedConfig,
 }
 
 // configFactoryFromAPIVersion checks that all configs in the input stream have the same API version, and returns a function to create a config with that API version.
-func configFactoryFromAPIVersion(buf []byte) (func() util.VersionedConfig, error) {
+func configFactoryFromAPIVersion(buf []byte) ([]func() util.VersionedConfig, error) {
 	// This is to quickly check that it's possibly a skaffold.yaml,
 	// without parsing the whole file.
 	if !bytes.Contains(buf, []byte("apiVersion")) {
 		return nil, errors.New("missing apiVersion")
 	}
 
-	var cfgVersions []APIVersion
+	var factories []func() util.VersionedConfig
 	b := bytes.NewReader(buf)
 	decoder := yaml.NewDecoder(b)
 	for {
@@ -230,25 +230,13 @@ func configFactoryFromAPIVersion(buf []byte) (func() util.VersionedConfig, error
 		if err != nil {
 			return nil, fmt.Errorf("parsing api version: %w", err)
 		}
-		cfgVersions = append(cfgVersions, v)
-	}
-
-	if len(cfgVersions) == 0 {
-		return nil, errors.New("invalid config")
-	}
-	apiVersion := cfgVersions[0].Version
-
-	for _, v := range cfgVersions {
-		if v.Version != apiVersion {
-			return nil, errors.New("multiple config versions detected in the same file")
+		factory, present := SchemaVersions.Find(v.Version)
+		if !present {
+			return nil, fmt.Errorf("unknown api version: %q", v.Version)
 		}
+		factories = append(factories, factory)
 	}
-
-	factory, present := SchemaVersions.Find(apiVersion)
-	if !present {
-		return nil, fmt.Errorf("unknown api version: %q", apiVersion)
-	}
-	return factory, nil
+	return factories, nil
 }
 
 // removeYamlAnchors removes all top-level keys starting with `.` from the input stream so they can be used as YAML anchors
@@ -285,13 +273,13 @@ func removeYamlAnchors(buf []byte) ([]byte, error) {
 	return out.Bytes(), nil
 }
 
-func parseConfig(buf []byte, factory func() util.VersionedConfig) ([]util.VersionedConfig, error) {
+func parseConfig(buf []byte, factories []func() util.VersionedConfig) ([]util.VersionedConfig, error) {
 	b := bytes.NewReader(buf)
 	decoder := yaml.NewDecoder(b)
 	decoder.KnownFields(true)
 	var cfgs []util.VersionedConfig
-	for {
-		cfg := factory()
+	for index := 0; index < len(factories); index++ {
+		cfg := factories[index]()
 		err := decoder.Decode(cfg)
 		if err == io.EOF {
 			break
diff --git a/pkg/skaffold/schema/versions_test.go b/pkg/skaffold/schema/versions_test.go
index f5e0913d6be..cc2f1479292 100644
--- a/pkg/skaffold/schema/versions_test.go
+++ b/pkg/skaffold/schema/versions_test.go
@@ -254,7 +254,7 @@ func TestParseConfigAndUpgrade(t *testing.T) {
 				withGoogleCloudBuild("ID",
 					withShaTagger(),
 					withDockerArtifact("image1", "./examples/app1", "Dockerfile.dev"),
-					withBazelArtifact("image2", "./examples/app2", "//:example.tar"),
+					withBazelArtifact(),
 				),
 				withKubectlDeploy("dep.yaml", "svc.yaml"),
 				withLogsPrefix("container"),
@@ -268,7 +268,7 @@ func TestParseConfigAndUpgrade(t *testing.T) {
 				withGoogleCloudBuild("ID",
 					withShaTagger(),
 					withDockerArtifact("image1", "./examples/app1", "Dockerfile.dev"),
-					withBazelArtifact("image2", "./examples/app2", "//:example.tar"),
+					withBazelArtifact(),
 				),
 				withKubectlDeploy("dep.yaml", "svc.yaml"),
 				withLogsPrefix("container"),
@@ -276,13 +276,35 @@ func TestParseConfigAndUpgrade(t *testing.T) {
 		},
 		{
 			apiVersion:  []string{latest.Version, latest.Version},
-			description: "Multiple complete config",
+			description: "Multiple complete config with same API versions",
 			config:      []string{completeConfig, completeClusterConfig},
 			expected: []util.VersionedConfig{config(
 				withGoogleCloudBuild("ID",
 					withShaTagger(),
 					withDockerArtifact("image1", "./examples/app1", "Dockerfile.dev"),
-					withBazelArtifact("image2", "./examples/app2", "//:example.tar"),
+					withBazelArtifact(),
+				),
+				withKubectlDeploy("dep.yaml", "svc.yaml"),
+				withLogsPrefix("container"),
+			), config(
+				withClusterBuild("secret-name", "/secret", "nskaniko", "/secret.json", "120m",
+					withGitTagger(),
+					withDockerConfig("config-name", "/kaniko/.docker"),
+					withKanikoArtifact(),
+				),
+				withKubectlDeploy("k8s/*.yaml"),
+				withLogsPrefix("container"),
+			)},
+		},
+		{
+			apiVersion:  []string{latest.Version, v2beta8.Version},
+			description: "Multiple complete config with different API versions",
+			config:      []string{completeConfig, completeClusterConfig},
+			expected: []util.VersionedConfig{config(
+				withGoogleCloudBuild("ID",
+					withShaTagger(),
+					withDockerArtifact("image1", "./examples/app1", "Dockerfile.dev"),
+					withBazelArtifact(),
 				),
 				withKubectlDeploy("dep.yaml", "svc.yaml"),
 				withLogsPrefix("container"),
@@ -341,12 +363,6 @@ func TestParseConfigAndUpgrade(t *testing.T) {
 			config:      []string{minimalConfig},
 			shouldErr:   true,
 		},
-		{
-			apiVersion:  []string{latest.Version, v2beta8.Version},
-			description: "ApiVersion mismatch",
-			config:      []string{simpleConfig, simpleConfig},
-			shouldErr:   true,
-		},
 		{
 			apiVersion:  []string{latest.Version},
 			description: "invalid statusCheckDeadline",
@@ -551,14 +567,14 @@ func withDockerArtifact(image, workspace, dockerfile string) func(*latest.BuildC
 	}
 }
 
-func withBazelArtifact(image, workspace, target string) func(*latest.BuildConfig) {
+func withBazelArtifact() func(*latest.BuildConfig) {
 	return func(cfg *latest.BuildConfig) {
 		cfg.Artifacts = append(cfg.Artifacts, &latest.Artifact{
-			ImageName: image,
-			Workspace: workspace,
+			ImageName: "image2",
+			Workspace: "./examples/app2",
 			ArtifactType: latest.ArtifactType{
 				BazelArtifact: &latest.BazelArtifact{
-					BuildTarget: target,
+					BuildTarget: "//:example.tar",
 				},
 			},
 		})