diff --git a/scripts/gendocs/generate b/scripts/gendocs/generate
index 5a25b6c5ba2..4ead5bd9620 100755
--- a/scripts/gendocs/generate
+++ b/scripts/gendocs/generate
@@ -63,18 +63,20 @@ gencliversions="${1:-0}"
 genversion() {
 	checkout "$1"
 	gendocs "$2"
+}
+
+genversionwithcli() {
+  genversion "$1" "$2"
+
+  genclireference "$2" "cmd/acmesolver" "acmesolver"
+  genclireference "$2" "cmd/cainjector" "cainjector"
+  genclireference "$2" "cmd/ctl" "cmctl"
+  genclireference "$2" "cmd/controller" "controller"
+  genclireference "$2" "cmd/webhook" "webhook"
 
-  if [ "$gencliversions" == 1 ]; then
-    genclireference "$2" "cmd/acmesolver" "acmesolver"
-    genclireference "$2" "cmd/cainjector" "cainjector"
-    genclireference "$2" "cmd/ctl" "cmctl"
-    genclireference "$2" "cmd/controller" "controller"
-    genclireference "$2" "cmd/webhook" "webhook"
-
-    # if any of the above steps succeeded copy over the index file
-    if [ -d "$REPO_ROOT/content/en/$2/cli" ]; then
-      cp "$REPO_ROOT/content/en/docs/cli/_index.md" "${REPO_ROOT}/content/en/$2/cli/"
-    fi
+  # if any of the above steps succeeded copy over the index file
+  if [ -d "$REPO_ROOT/content/en/$2/cli" ]; then
+    cp "$REPO_ROOT/content/en/docs/cli/_index.md" "${REPO_ROOT}/content/en/$2/cli/"
   fi
 }
 
@@ -142,21 +144,27 @@ $output
 EOF
 }
 
+# The branches named here exist in the `jetstack/cert-manager` repo.
+
+genversionwithcli "release-1.7" "next-docs"
+
+checkout "release-1.6"
+
+# At the top of this script we pull the repository from the latest from master.
+# These commands must follow an explicit checkout of the latest release,
+# otherwise unreleased CLI flags are included.
+# For 1.6 they must happen before removing the legacy APIs
+# as it will not compile without them.
 genclireference "docs" "cmd/acmesolver" "acmesolver"
 genclireference "docs" "cmd/cainjector" "cainjector"
 genclireference "docs" "cmd/ctl" "cmctl"
 genclireference "docs" "cmd/controller" "controller"
 genclireference "docs" "cmd/webhook" "webhook"
 
-# The branches named here exist in the `jetstack/cert-manager` repo.
-
-genversion "release-1.7" "next-docs"
-
 # In cert-manager 1.6 cert-manager.io and acme.cert-manager.io alpha and beta
 # API versions are no longer served, but the apis are still in the codebase. We
 # don't want to show the docs for those API versions so this is a workaround.
 # This will only be necessary for the release-1.6 branch.
-checkout "release-1.6"
 rm -r pkg/apis/acme/v1alpha2
 rm -r pkg/apis/acme/v1alpha3
 rm -r pkg/apis/acme/v1beta1
@@ -174,9 +182,10 @@ rm -r pkg/apis/certmanager/v1alpha3
 rm -r pkg/apis/certmanager/v1beta1
 gendocs "v1.6-docs"
 
-# when adding a new version here run
-# ./scripts/gendocs/generate 1 to force generation of CLI docs
-# and add them to the git index
+# from 1.7 and onward:
+# when adding a new version here use
+# genversionwithcli, for example:
+# genversionwithcli "release-1.6" "v1.6-docs"
 genversion "release-1.5" "v1.5-docs"
 genversion "release-1.4" "v1.4-docs"
 genversion "release-1.3" "v1.3-docs"