I am using happily deployments from GitHub to Azure functions, but I wanted to use a repo I have in another Organizations collection. I came across this article : https://azure.microsoft.com/en-us/blog/using-app-service-web-apps-continuous-deployment-with-github-organizations/ which is currently just partially true, because GitHub UI changed a bit.
In Installed GitHub apps where the Azure Management Portal app should be I see 0 apps :
but Authorized OAuth Apps is now the tab where you should go.
and clicking on the name of app (Azure Management Portal) you will now see a list of your organizations that could be granted to be listed in your account (here I already granted access for one ogranization):
Now in http://portal.azure.com you could see something like this :
Hope this helps.