diff --git a/pkg/base/render.go b/pkg/base/render.go
index 200308c3a3..0c003c51b6 100644
--- a/pkg/base/render.go
+++ b/pkg/base/render.go
@@ -14,6 +14,7 @@ type RenderOptions struct {
 	LocalRegistryNamespace string
 	LocalRegistryUsername  string
 	LocalRegistryPassword  string
+	ExcludeKotsKinds       bool
 	Log                    *logger.Logger
 }
 
diff --git a/pkg/base/replicated.go b/pkg/base/replicated.go
index c5b768e214..7008a13e48 100644
--- a/pkg/base/replicated.go
+++ b/pkg/base/replicated.go
@@ -98,7 +98,16 @@ func renderReplicated(u *upstreamtypes.Upstream, renderOptions *RenderOptions) (
 			return nil, errors.Wrapf(err, "failed to convert upstream file %s to base", upstreamFile.Path)
 		}
 
-		base.Files = append(base.Files, baseFile)
+		baseFiles := convertToSingleDocs([]BaseFile{baseFile})
+		for _, f := range baseFiles {
+			include, err := f.ShouldBeIncludedInBaseKustomization(renderOptions.ExcludeKotsKinds)
+			if err != nil {
+				return nil, errors.Wrapf(err, "failed to check if base file %s should be included", f.Path)
+			}
+			if include {
+				base.Files = append(base.Files, f)
+			}
+		}
 	}
 
 	// render helm charts that were specified
@@ -186,6 +195,7 @@ func renderReplicated(u *upstreamtypes.Upstream, renderOptions *RenderOptions) (
 			SplitMultiDocYAML: true,
 			Namespace:         namespace,
 			HelmOptions:       localValues,
+			ExcludeKotsKinds:  renderOptions.ExcludeKotsKinds,
 			Log:               nil,
 		})
 		if err != nil {
diff --git a/pkg/pull/pull.go b/pkg/pull/pull.go
index 8720ce9988..3fa7b29e4c 100644
--- a/pkg/pull/pull.go
+++ b/pkg/pull/pull.go
@@ -236,6 +236,7 @@ func Pull(upstreamURI string, pullOptions PullOptions) (string, error) {
 		LocalRegistryNamespace: pullOptions.RewriteImageOptions.Namespace,
 		LocalRegistryUsername:  pullOptions.RewriteImageOptions.Username,
 		LocalRegistryPassword:  pullOptions.RewriteImageOptions.Password,
+		ExcludeKotsKinds:       pullOptions.ExcludeKotsKinds,
 		Log:                    log,
 	}
 	log.ActionWithSpinner("Creating base")
diff --git a/pkg/rewrite/rewrite.go b/pkg/rewrite/rewrite.go
index 63830a4f49..6185f4a010 100644
--- a/pkg/rewrite/rewrite.go
+++ b/pkg/rewrite/rewrite.go
@@ -94,6 +94,7 @@ func Rewrite(rewriteOptions RewriteOptions) error {
 		LocalRegistryNamespace: rewriteOptions.RegistryNamespace,
 		LocalRegistryUsername:  rewriteOptions.RegistryUsername,
 		LocalRegistryPassword:  rewriteOptions.RegistryPassword,
+		ExcludeKotsKinds:       rewriteOptions.ExcludeKotsKinds,
 		Log:                    log,
 	}
 	log.ActionWithSpinner("Creating base")