diff --git a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/AROSwift/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/AROSwift/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
index 2d9b1f3026d..fb3ee8bbb26 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/AROSwift/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/AROSwift/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
@@ -137,12 +137,6 @@ spec:
           rm -f /var/payload/manifests/*_deployment.yaml
           rm -f /var/payload/manifests/*_servicemonitor.yaml
           cp -R /release-manifests /var/payload/
-          for file in $(find /var/payload/manifests/ -name "*.yaml"); do
-              IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-              if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "Default" ]]; then
-                  rm -vf $file
-              fi
-          done
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-config.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-rbac.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-secret.yaml
@@ -306,13 +300,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/GCP/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/GCP/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
index 1b3c7f44f78..0a5070f2c81 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/GCP/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/GCP/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
@@ -148,12 +148,6 @@ spec:
           rm -f /var/payload/manifests/*_deployment.yaml
           rm -f /var/payload/manifests/*_servicemonitor.yaml
           cp -R /release-manifests /var/payload/
-          for file in $(find /var/payload/manifests/ -name "*.yaml"); do
-              IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-              if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "TechPreviewNoUpgrade" ]]; then
-                  rm -vf $file
-              fi
-          done
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-config.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-rbac.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-secret.yaml
@@ -323,13 +317,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/IBMCloud/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/IBMCloud/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
index 553aad2bbe4..5d4a8451a8c 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/IBMCloud/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/IBMCloud/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
@@ -137,12 +137,6 @@ spec:
           rm -f /var/payload/manifests/*_deployment.yaml
           rm -f /var/payload/manifests/*_servicemonitor.yaml
           cp -R /release-manifests /var/payload/
-          for file in $(find /var/payload/manifests/ -name "*.yaml"); do
-              IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-              if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "Default" ]]; then
-                  rm -vf $file
-              fi
-          done
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-config.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-rbac.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-secret.yaml
@@ -243,13 +237,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/TechPreviewNoUpgrade/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/TechPreviewNoUpgrade/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
index e1230b097c4..fb3ee8bbb26 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/TechPreviewNoUpgrade/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/TechPreviewNoUpgrade/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
@@ -137,12 +137,6 @@ spec:
           rm -f /var/payload/manifests/*_deployment.yaml
           rm -f /var/payload/manifests/*_servicemonitor.yaml
           cp -R /release-manifests /var/payload/
-          for file in $(find /var/payload/manifests/ -name "*.yaml"); do
-              IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-              if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "TechPreviewNoUpgrade" ]]; then
-                  rm -vf $file
-              fi
-          done
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-config.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-rbac.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-secret.yaml
@@ -306,13 +300,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
index 2d9b1f3026d..fb3ee8bbb26 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/testdata/cluster-version-operator/zz_fixture_TestControlPlaneComponents_cluster_version_operator_deployment.yaml
@@ -137,12 +137,6 @@ spec:
           rm -f /var/payload/manifests/*_deployment.yaml
           rm -f /var/payload/manifests/*_servicemonitor.yaml
           cp -R /release-manifests /var/payload/
-          for file in $(find /var/payload/manifests/ -name "*.yaml"); do
-              IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-              if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "Default" ]]; then
-                  rm -vf $file
-              fi
-          done
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-config.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-rbac.yaml
           rm -f /var/payload/release-manifests/0000_50_olm_00-pprof-secret.yaml
@@ -306,13 +300,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/v2/assets/cluster-version-operator/deployment.yaml b/control-plane-operator/controllers/hostedcontrolplane/v2/assets/cluster-version-operator/deployment.yaml
index f43b002ccda..2880ab4ef68 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/v2/assets/cluster-version-operator/deployment.yaml
+++ b/control-plane-operator/controllers/hostedcontrolplane/v2/assets/cluster-version-operator/deployment.yaml
@@ -91,13 +91,11 @@ spec:
           cat > /tmp/clusterversion.json <<EOF
           ${CLUSTER_VERSION_JSON}
           EOF
-          oc get ns openshift-config &> /dev/null || oc create ns openshift-config
-          oc get ns openshift-config-managed &> /dev/null || oc create ns openshift-config-managed
-          oc apply -f /var/payload/manifests/0000_00_cluster-version-operator_01_clusterversions*
-          oc apply -f /tmp/clusterversion.json
-          while true; do
+          echo 'Deciding whether bootstrap resources need to be applied...'
+          ls -l $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests) /tmp/clusterversion.json
+          while test -z "$(oc get -o jsonpath='{.status.history[0].version}' clusterversions.config.openshift.io version)"; do
             echo "Applying CVO bootstrap manifests..."
-            if oc apply -f /var/payload/manifests; then
+            if oc apply $(grep -rl 'include.release.openshift.io/bootstrap-cluster-version-operator: .*hypershift' /var/payload/manifests | sed 's/^/-f /') -f /tmp/clusterversion.json; then
               echo "Bootstrap manifests applied successfully."
               break
             fi
diff --git a/control-plane-operator/controllers/hostedcontrolplane/v2/cvo/deployment.go b/control-plane-operator/controllers/hostedcontrolplane/v2/cvo/deployment.go
index 56c175e9868..d74df2b1103 100644
--- a/control-plane-operator/controllers/hostedcontrolplane/v2/cvo/deployment.go
+++ b/control-plane-operator/controllers/hostedcontrolplane/v2/cvo/deployment.go
@@ -204,18 +204,6 @@ func preparePayloadScript(platformType hyperv1.PlatformType, oauthEnabled bool,
 		fmt.Sprintf("cp -R /release-manifests %s/", payloadDir),
 	)
 
-	// NOTE: We would need to leverage part of the manifest.Include logic (https://github.com/openshift/library-go/blob/0064ad7bd060b9fd52f7840972c1d3e72186d0f0/pkg/manifest/manifest.go#L190-L196)
-	// to properly evaluate which CVO manifests to select based on featureset.
-	// We only have access to bash, so we must filter based on the feature-set annotation in the manifests manually.
-	// Any file that has a feature-set annotation must have a value that matches the current feature set else it is removed.
-	// Files that do not have a feature-set annotation are included unconditionally.
-	stmts = append(stmts, fmt.Sprintf(`for file in $(find %s/manifests/ -name "*.yaml"); do
-    IFS=',' read -ra feature_sets <<< "$(cat $file | grep "release.openshift.io/feature-set:" | awk '{print $2}')"
-    if [[ "${#feature_sets[@]}" -gt 0 ]] && ! [[ " ${feature_sets[*]} " =~ "%s" ]]; then
-        rm -vf $file
-    fi
-done`, payloadDir, featureSet))
-
 	for _, manifest := range manifestsToOmit {
 		if platformType == hyperv1.IBMCloudPlatform || platformType == hyperv1.PowerVSPlatform {
 			if manifest == "0000_50_cluster-storage-operator_10_deployment-ibm-cloud-managed.yaml" || manifest == "0000_50_cluster-csi-snapshot-controller-operator_07_deployment-ibm-cloud-managed.yaml" {