diff --git a/fabric-ca/makeDocker.sh b/fabric-ca/makeDocker.sh
index 4ca3e946d3..f55bbba416 100755
--- a/fabric-ca/makeDocker.sh
+++ b/fabric-ca/makeDocker.sh
@@ -133,6 +133,7 @@ function writeRootCA {
       - FABRIC_CA_SERVER_DEBUG=true
       - BOOTSTRAP_USER_PASS=$ROOT_CA_ADMIN_USER_PASS
       - TARGET_CERTFILE=$ROOT_CA_CERTFILE
+      - FABRIC_ORGS="$ORGS"
     volumes:
       - ./scripts:/scripts
       - ./$DATA:/$DATA
@@ -157,6 +158,7 @@ function writeIntermediateCA {
       - PARENT_URL=https://$ROOT_CA_ADMIN_USER_PASS@$ROOT_CA_HOST:7054
       - TARGET_CHAINFILE=$INT_CA_CHAINFILE
       - ORG=$ORG
+      - FABRIC_ORGS="$ORGS"
     volumes:
       - ./scripts:/scripts
       - ./$DATA:/$DATA
diff --git a/fabric-ca/scripts/start-intermediate-ca.sh b/fabric-ca/scripts/start-intermediate-ca.sh
index 9aaff554c1..01bf14b931 100755
--- a/fabric-ca/scripts/start-intermediate-ca.sh
+++ b/fabric-ca/scripts/start-intermediate-ca.sh
@@ -19,5 +19,13 @@ fabric-ca-server init -b $BOOTSTRAP_USER_PASS -u $PARENT_URL
 # Copy the intermediate CA's certificate chain to the data directory to be used by others
 cp $FABRIC_CA_SERVER_HOME/ca-chain.pem $TARGET_CHAINFILE
 
+# Add the custom orgs
+for o in $FABRIC_ORGS; do
+   aff=$aff"\n   $o: []"
+done
+aff="${aff#\\n   }"
+sed -i "/affiliations:/a \\   $aff" \
+   $FABRIC_CA_SERVER_HOME/fabric-ca-server-config.yaml
+
 # Start the intermediate CA
 fabric-ca-server start
diff --git a/fabric-ca/scripts/start-root-ca.sh b/fabric-ca/scripts/start-root-ca.sh
index 27874ddf60..f1fa244b1a 100755
--- a/fabric-ca/scripts/start-root-ca.sh
+++ b/fabric-ca/scripts/start-root-ca.sh
@@ -13,5 +13,13 @@ fabric-ca-server init -b $BOOTSTRAP_USER_PASS
 # Copy the root CA's signing certificate to the data directory to be used by others
 cp $FABRIC_CA_SERVER_HOME/ca-cert.pem $TARGET_CERTFILE
 
+# Add the custom orgs
+for o in $FABRIC_ORGS; do
+   aff=$aff"\n   $o: []"
+done
+aff="${aff#\\n   }"
+sed -i "/affiliations:/a \\   $aff" \
+   $FABRIC_CA_SERVER_HOME/fabric-ca-server-config.yaml
+
 # Start the root CA
 fabric-ca-server start