Storing your environment data or secrets in Datastore, in a bucket using 
GCS may be rather considered as the usual thing to do in this environment. 
More about the encryption capabilities of the platform can be read in the 
"Encryption at Rest" document 
<https://cloud.google.com/security/encryption-at-rest/>. 

App Engine allows you to make use of appropriate services, that provide you 
with tools allowing to store safely configuration and secrets. Cloud KMS is 
a REST API that can use a key to encrypt or decrypt data, such as secrets, 
for storage. You may read details on the "CLOUD KEY MANAGEMENT SERVICE" 
documentation page <https://cloud.google.com/kms/>. 

You may be interested in the  "App Identity API 
<https://cloud.google.com/appengine/docs/standard/java/appidentity/#Java_Asserting_identity_to_other_systems>"
 
as well. 

Environment variables can be made available to the app by specifying them 
at deployment time in the app.yaml file, as describe in the "Configuring 
your App with app.yaml" documentation page 
<https://cloud.google.com/appengine/docs/flexible/nodejs/configuring-your-app-with-app-yaml>,
 
both for flex and standard environments. 

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