diff --git a/templates/test/ci/cluster-template-prow-ci-version-windows.yaml b/templates/test/ci/cluster-template-prow-ci-version-windows.yaml
index ff0322a93343..b4d3fc7ece27 100644
--- a/templates/test/ci/cluster-template-prow-ci-version-windows.yaml
+++ b/templates/test/ci/cluster-template-prow-ci-version-windows.yaml
@@ -42,10 +42,6 @@ metadata:
   name: ${CLUSTER_NAME}-control-plane
   namespace: default
 spec:
-  infrastructureTemplate:
-    apiVersion: infrastructure.cluster.x-k8s.io/v1alpha4
-    kind: AzureMachineTemplate
-    name: ${CLUSTER_NAME}-control-plane
   kubeadmConfigSpec:
     clusterConfiguration:
       apiServer:
@@ -198,6 +194,11 @@ spec:
     preKubeadmCommands:
     - bash -c /tmp/kubeadm-bootstrap.sh
     useExperimentalRetryJoin: true
+  machineTemplate:
+    infrastructureRef:
+      apiVersion: infrastructure.cluster.x-k8s.io/v1alpha4
+      kind: AzureMachineTemplate
+      name: ${CLUSTER_NAME}-control-plane
   replicas: ${CONTROL_PLANE_MACHINE_COUNT}
   version: ${KUBERNETES_VERSION}
 ---
@@ -232,9 +233,8 @@ metadata:
   namespace: default
 spec:
   clusterName: ${CLUSTER_NAME}
-  replicas: ${WORKER_MACHINE_COUNT}
-  selector:
-    matchLabels: null
+  replicas: "0"
+  selector: {}
   template:
     spec:
       bootstrap:
diff --git a/templates/test/ci/cluster-template-prow-windows.yaml b/templates/test/ci/cluster-template-prow-windows.yaml
index 8fc8c5de3ae1..2071d2c5a483 100644
--- a/templates/test/ci/cluster-template-prow-windows.yaml
+++ b/templates/test/ci/cluster-template-prow-windows.yaml
@@ -161,9 +161,8 @@ metadata:
   namespace: default
 spec:
   clusterName: ${CLUSTER_NAME}
-  replicas: ${WORKER_MACHINE_COUNT}
-  selector:
-    matchLabels: null
+  replicas: "0"
+  selector: {}
   template:
     spec:
       bootstrap:
diff --git a/templates/test/ci/prow-windows/kustomization.yaml b/templates/test/ci/prow-windows/kustomization.yaml
index cb85ba227603..c199d8a17b1e 100644
--- a/templates/test/ci/prow-windows/kustomization.yaml
+++ b/templates/test/ci/prow-windows/kustomization.yaml
@@ -8,6 +8,7 @@ patchesStrategicMerge:
   - ../patches/tags.yaml
   - ../patches/cluster-cni-windows.yaml
   - ../patches/controller-manager.yaml
+  - patches/drop-linux-pool.yaml
 patchesJson6902:
 - target:
     group: bootstrap.cluster.x-k8s.io
diff --git a/templates/test/ci/prow-windows/patches/drop-linux-pool.yaml b/templates/test/ci/prow-windows/patches/drop-linux-pool.yaml
new file mode 100644
index 000000000000..aee5981a0da4
--- /dev/null
+++ b/templates/test/ci/prow-windows/patches/drop-linux-pool.yaml
@@ -0,0 +1,10 @@
+apiVersion: cluster.x-k8s.io/v1alpha4
+kind: MachineDeployment
+metadata:
+  name: ${CLUSTER_NAME}-md-0
+  namespace: default
+spec:
+  # For upstream prow jobs we don't need Linux pools
+  # the templates are based off the base windows template
+  # and kustomize doesn't allow remove resources.
+  replicas: 0
\ No newline at end of file
diff --git a/templates/test/dev/cluster-template-custom-builds-windows.yaml b/templates/test/dev/cluster-template-custom-builds-windows.yaml
index f2efdd69870f..31e3809e21ae 100644
--- a/templates/test/dev/cluster-template-custom-builds-windows.yaml
+++ b/templates/test/dev/cluster-template-custom-builds-windows.yaml
@@ -44,10 +44,6 @@ metadata:
   name: ${CLUSTER_NAME}-control-plane
   namespace: default
 spec:
-  infrastructureTemplate:
-    apiVersion: infrastructure.cluster.x-k8s.io/v1alpha4
-    kind: AzureMachineTemplate
-    name: ${CLUSTER_NAME}-control-plane
   kubeadmConfigSpec:
     clusterConfiguration:
       apiServer:
@@ -173,6 +169,11 @@ spec:
     preKubeadmCommands:
     - bash -c /tmp/replace-k8s-binaries.sh
     useExperimentalRetryJoin: true
+  machineTemplate:
+    infrastructureRef:
+      apiVersion: infrastructure.cluster.x-k8s.io/v1alpha4
+      kind: AzureMachineTemplate
+      name: ${CLUSTER_NAME}-control-plane
   replicas: ${CONTROL_PLANE_MACHINE_COUNT}
   version: ${KUBERNETES_VERSION}
 ---
@@ -207,9 +208,8 @@ metadata:
   namespace: default
 spec:
   clusterName: ${CLUSTER_NAME}
-  replicas: ${WORKER_MACHINE_COUNT}
-  selector:
-    matchLabels: null
+  replicas: "0"
+  selector: {}
   template:
     spec:
       bootstrap: