diff --git a/tools/document/validate_site_docs.sh b/tools/document/validate_site_docs.sh
index 8e6569213..1a19a4c00 100755
--- a/tools/document/validate_site_docs.sh
+++ b/tools/document/validate_site_docs.sh
@@ -14,7 +14,14 @@
 
 set -e
 
-: ${PROJECT_ROOT:=${PWD}}
+# The root of the manifest structure to be validated.
+# This corresponds to the targetPath in an airshipctl config
+: ${MANIFEST_ROOT:="${PWD}"}
+# The location of sites whose manifests should be validated.
+# This are relative to MANIFEST_ROOT above, and correspond to
+# the base of the subPath in an airshipctl config
+: ${SITE_ROOT:="manifests/site"}
+
 : ${SITE:="test-workload"}
 : ${CONTEXT:="kind-airship"}
 : ${KUBECONFIG:="${HOME}/.airship/kubeconfig"}
@@ -89,8 +96,8 @@ manifests:
           force: false
           tag: ""
         url: https://opendev.org/airship/treasuremap
-    subPath: manifests/site/${SITE}
-    targetPath: .
+    subPath: ${SITE_ROOT}/${SITE}
+    targetPath: ${MANIFEST_ROOT}
 users:
   ${CONTEXT}_${cluster}: {}
 EOL
@@ -104,7 +111,7 @@ trap cleanup EXIT
 
 # Loop over all cluster types and phases for the given site
 for cluster in ephemeral target; do
-    if [[ -d "manifests/site/${SITE}/${cluster}" ]]; then
+    if [[ -d "${MANIFEST_ROOT}/${SITE_ROOT}/${SITE}/${cluster}" ]]; then
         echo -e "\n**** Rendering phases for cluster: ${cluster}"
         # Start a fresh, empty kind cluster for validating documents
         ./tools/document/start_kind.sh
@@ -126,7 +133,7 @@ for cluster in ephemeral target; do
 
         for phase in $phases; do
             # Guard against bootstrap or initinfra being missing, which could be the case for some configs
-            if [ -d "manifests/site/${SITE}/${cluster}/${phase}" ]; then
+            if [ -d "${MANIFEST_ROOT}/${SITE_ROOT}/${SITE}/${cluster}/${phase}" ]; then
                 echo -e "\n*** Rendering ${cluster}/${phase}"
 
                 # step 1: actually apply all crds in the phase
diff --git a/tools/validate_docs b/tools/validate_docs
index b0bb7083c..4edbfc505 100755
--- a/tools/validate_docs
+++ b/tools/validate_docs
@@ -16,6 +16,14 @@
 # Expected to be run from the project root
 set -xe
 
+# The root of the manifest structure to be validated.
+# This corresponds to the targetPath in an airshipctl config
+: ${MANIFEST_ROOT:="${PWD}"}
+# The space-separated locations of sites whose manifests should be validated.
+# These are relative to MANIFEST_ROOT above, and correspond to
+# the base of the subPath in an airshipctl config
+: ${SITE_ROOTS:="manifests/site"}
+
 # get kind
 echo "Fetching kind from ${KIND_URL}..."
 TMP=$(KIND_URL=${KIND_URL} ./tools/document/get_kind.sh)
@@ -24,9 +32,12 @@ export KUBECTL_URL
 
 ./tools/document/build_kustomize_plugin.sh
 
-for site in $(ls manifests/site); do
-    echo -e "\nValidating site: ${site}\n****************"
-    SITE=${site} ./tools/document/validate_site_docs.sh
-    echo "Validation of site ${site} is succesful!"
+for site_root in ${SITE_ROOTS}; do
+  for site in $(ls ${MANIFEST_ROOT}/${site_root}); do
+      echo -e "\nValidating site: ${MANIFEST_ROOT}/${site_root}/${site}\n****************"
+      MANIFEST_ROOT=${MANIFEST_ROOT} SITE_ROOT=${site_root} SITE=${site} \
+        ./tools/document/validate_site_docs.sh
+      echo "Validation of site ${site} is succesful!"
+  done
 done