diff --git a/manifests/composite/infra/replacements/kustomization.yaml b/manifests/composite/infra/replacements/kustomization.yaml
new file mode 100644
index 000000000..66cce757a
--- /dev/null
+++ b/manifests/composite/infra/replacements/kustomization.yaml
@@ -0,0 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - ../../../function/cni/tigera-operator/replacements
+  - ../../../function/cert-manager/replacements
diff --git a/manifests/function/airshipctl-base-catalogues/versions-airshipctl.yaml b/manifests/function/airshipctl-base-catalogues/versions-airshipctl.yaml
index 11167c6c3..741694601 100644
--- a/manifests/function/airshipctl-base-catalogues/versions-airshipctl.yaml
+++ b/manifests/function/airshipctl-base-catalogues/versions-airshipctl.yaml
@@ -146,8 +146,11 @@ spec:
         manager:
           image: ghcr.io/fluxcd/source-controller:v0.5.3
     cert-manager:
-      cert-manager:
-        repository:
-          image: "quay.io/jetstack"
+      cainjector:
+        image: quay.io/jetstack/cert-manager-cainjector:v1.1.0
+      controller:
+        image: quay.io/jetstack/cert-manager-controller:v1.1.0
+      webhook:
+        image: quay.io/jetstack/cert-manager-webhook:v1.1.0
 
   kubernetes: v1.18.6
diff --git a/manifests/function/cert-manager/replacements/kustomization.yaml b/manifests/function/cert-manager/replacements/kustomization.yaml
new file mode 100644
index 000000000..1d43ee154
--- /dev/null
+++ b/manifests/function/cert-manager/replacements/kustomization.yaml
@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - versions.yaml
diff --git a/manifests/function/cert-manager/replacements/versions.yaml b/manifests/function/cert-manager/replacements/versions.yaml
new file mode 100644
index 000000000..c77be7e17
--- /dev/null
+++ b/manifests/function/cert-manager/replacements/versions.yaml
@@ -0,0 +1,39 @@
+apiVersion: airshipit.org/v1alpha1
+kind: ReplacementTransformer
+metadata:
+  name: cert-manager-versions-replacements
+  annotations:
+    config.kubernetes.io/function: |-
+      container:
+        image: localhost/replacement-transformer
+replacements:
+- source:
+    objref:
+      kind: VersionsCatalogue
+      name: versions-airshipctl
+    fieldref: spec.images.cert-manager.cainjector.image
+  target:
+    objref:
+      kind: Deployment
+      name: cert-manager-cainjector
+    fieldrefs: ["spec.template.spec.containers[name=cert-manager].image"]
+- source:
+    objref:
+      kind: VersionsCatalogue
+      name: versions-airshipctl
+    fieldref: spec.images.cert-manager.controller.image
+  target:
+    objref:
+      kind: Deployment
+      name: cert-manager
+    fieldrefs: ["spec.template.spec.containers[name=cert-manager].image"]
+- source:
+    objref:
+      kind: VersionsCatalogue
+      name: versions-airshipctl
+    fieldref: spec.images.cert-manager.webhook.image
+  target:
+    objref:
+      kind: Deployment
+      name: cert-manager-webhook
+    fieldrefs: ["spec.template.spec.containers[name=cert-manager].image"]
diff --git a/manifests/function/clusterctl/replacements/versions.yaml b/manifests/function/clusterctl/replacements/versions.yaml
index afd3bbff5..2c967f661 100644
--- a/manifests/function/clusterctl/replacements/versions.yaml
+++ b/manifests/function/clusterctl/replacements/versions.yaml
@@ -187,15 +187,3 @@ replacements:
       kind: Clusterctl
       name: clusterctl_init
     fieldrefs: ["{.images.infrastructure-azure/kube-rbac-proxy}"]
-
-# Replace the cert-manager image repository in the Clusterctl
-- source:
-    objref:
-      kind: VersionsCatalogue
-      name: versions-airshipctl
-    fieldref: "{.spec.images.cert-manager.cert-manager.repository.image}"
-  target:
-    objref:
-      kind: Clusterctl
-      name: clusterctl_init
-    fieldrefs: ["{.images.cert-manager.repository}"]
diff --git a/manifests/site/docker-test-site/target/catalogues/kustomization.yaml b/manifests/site/docker-test-site/target/catalogues/kustomization.yaml
new file mode 100644
index 000000000..5c4965841
--- /dev/null
+++ b/manifests/site/docker-test-site/target/catalogues/kustomization.yaml
@@ -0,0 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+resources:
+  - ../../../../function/airshipctl-base-catalogues
diff --git a/manifests/site/docker-test-site/target/initinfra-networking/kustomization.yaml b/manifests/site/docker-test-site/target/initinfra-networking/kustomization.yaml
index 068decced..34e94f96e 100644
--- a/manifests/site/docker-test-site/target/initinfra-networking/kustomization.yaml
+++ b/manifests/site/docker-test-site/target/initinfra-networking/kustomization.yaml
@@ -1,6 +1,10 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
+  - ../catalogues
   - ../../../../composite/infra
 commonLabels:
   airshipit.org/stage: initinfra
+
+transformers:
+  - ../../../../composite/infra/replacements
diff --git a/manifests/site/gcp-test-site/target/catalogues/kustomization.yaml b/manifests/site/gcp-test-site/target/catalogues/kustomization.yaml
new file mode 100644
index 000000000..5c4965841
--- /dev/null
+++ b/manifests/site/gcp-test-site/target/catalogues/kustomization.yaml
@@ -0,0 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+resources:
+  - ../../../../function/airshipctl-base-catalogues
diff --git a/manifests/site/gcp-test-site/target/initinfra-networking/kustomization.yaml b/manifests/site/gcp-test-site/target/initinfra-networking/kustomization.yaml
index 37c98fc0f..067f41eba 100644
--- a/manifests/site/gcp-test-site/target/initinfra-networking/kustomization.yaml
+++ b/manifests/site/gcp-test-site/target/initinfra-networking/kustomization.yaml
@@ -1,7 +1,11 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
+  - ../catalogues
   - ../../../../composite/infra
 
 commonLabels:
   airshipit.org/stage: initinfra
+
+transformers:
+  - ../../../../composite/infra/replacements
diff --git a/manifests/site/openstack-test-site/target/catalogues/kustomization.yaml b/manifests/site/openstack-test-site/target/catalogues/kustomization.yaml
new file mode 100644
index 000000000..5c4965841
--- /dev/null
+++ b/manifests/site/openstack-test-site/target/catalogues/kustomization.yaml
@@ -0,0 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+resources:
+  - ../../../../function/airshipctl-base-catalogues
diff --git a/manifests/site/openstack-test-site/target/initinfra/kustomization.yaml b/manifests/site/openstack-test-site/target/initinfra/kustomization.yaml
index 37c98fc0f..184c7f0df 100644
--- a/manifests/site/openstack-test-site/target/initinfra/kustomization.yaml
+++ b/manifests/site/openstack-test-site/target/initinfra/kustomization.yaml
@@ -1,7 +1,12 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
+  - ../catalogues
   - ../../../../composite/infra
 
 commonLabels:
   airshipit.org/stage: initinfra
+
+transformers:
+  - ../../../../composite/infra/replacements
+
diff --git a/manifests/site/test-site/ephemeral/initinfra-networking/kustomization.yaml b/manifests/site/test-site/ephemeral/initinfra-networking/kustomization.yaml
index 25e1bfab6..5f471cde1 100644
--- a/manifests/site/test-site/ephemeral/initinfra-networking/kustomization.yaml
+++ b/manifests/site/test-site/ephemeral/initinfra-networking/kustomization.yaml
@@ -1,5 +1,9 @@
 resources:
+  - ../catalogues
   - ../../../../composite/infra/
 
 commonLabels:
   airshipit.org/stage: initinfra
+
+transformers:
+  - ../../../../composite/infra/replacements
diff --git a/manifests/site/test-site/target/initinfra-networking/kustomization.yaml b/manifests/site/test-site/target/initinfra-networking/kustomization.yaml
index 0381d98a9..256a7e540 100644
--- a/manifests/site/test-site/target/initinfra-networking/kustomization.yaml
+++ b/manifests/site/test-site/target/initinfra-networking/kustomization.yaml
@@ -1,6 +1,11 @@
 resources:
+  - ../catalogues
   - ../../../../composite/infra/
   - namespace.yaml
 
 commonLabels:
   airshipit.org/stage: initinfra
+
+transformers:
+  - ../../../../composite/infra/replacements
+