diff --git a/lib/utils.js b/lib/utils.js
index 0c6ae55..6ab6117 100644
--- a/lib/utils.js
+++ b/lib/utils.js
@@ -372,17 +372,19 @@ function saveAndReplaceDotEnvCredentials (dotenvFile, saveFile, apihost, namespa
   // Only override needed env vars and preserve other vars in .env
   const env = dotenv.parse(fs.readFileSync(saveFile))
   const newCredentials = {
-    AIO_RUNTIME_NAMESPACE: namespace,
-    AIO_RUNTIME_AUTH: auth,
-    AIO_RUNTIME_APIHOST: apihost
+    RUNTIME_NAMESPACE: namespace,
+    RUNTIME_AUTH: auth,
+    RUNTIME_APIHOST: apihost
   }
 
   // remove old keys (match by normalized key name)
   for (const key in env) {
-    const match = key.match(/^AIO_(.+)/i)
+    // match AIO_ or AIO__ since they map to the same key
+    // see https://github.com/adobe/aio-lib-core-config/issues/49
+    const match = key.match(/^AIO__(.+)/i) || key.match(/^AIO_(.+)/i)
     if (match) {
       for (const newCredential in newCredentials) {
-        if (newCredential.toLowerCase() === key.toLowerCase()) {
+        if (newCredential.toLowerCase() === match[1].toLowerCase()) {
           delete env[key]
         }
       }
@@ -391,7 +393,7 @@ function saveAndReplaceDotEnvCredentials (dotenvFile, saveFile, apihost, namespa
 
   // set the new keys
   for (const key in newCredentials) {
-    env[key] = newCredentials[key]
+    env[`AIO_${key}`] = newCredentials[key]
   }
 
   const envContent = Object.keys(env).reduce((content, k) => content + `${k}=${env[k]}\n`, '')
diff --git a/test/__fixtures__/app-env/my-env.expected b/test/__fixtures__/app-env/my-env.expected
index 6615e87..3a3c33f 100644
--- a/test/__fixtures__/app-env/my-env.expected
+++ b/test/__fixtures__/app-env/my-env.expected
@@ -1,3 +1,4 @@
+FOO=bar
 AIO_RUNTIME_NAMESPACE=local-namespace
 AIO_RUNTIME_AUTH=local-auth
 AIO_RUNTIME_APIHOST=local-apihost
diff --git a/test/__fixtures__/app-env/my-env.original b/test/__fixtures__/app-env/my-env.original
index b479b40..a857007 100644
--- a/test/__fixtures__/app-env/my-env.original
+++ b/test/__fixtures__/app-env/my-env.original
@@ -1,3 +1,7 @@
+FOO=bar
 AIO_runtime_namespace=my-remote-namespace
 AIO_runtime_auth=my-remote-auth
 AIO_runtime_apihost=my-remote-apihost
+AIO__runtime_namespace=my-remote-namespace2
+AIO__runtime_auth=my-remote-auth2
+AIO__runtime_apihost=my-remote-apihost2