When you deploy your web app to Azure, the AppSettingsSecrets.config file won't be deployed (that's what you want). You could go to the Azure Management Portal and set them manually, to do that:Go to http://portal.azure.com, and sign in with your Azure credentials. Click Browse > Web Apps, then click the name of your web app. Click All settings > Application settings.The app settings and connection string values override the same settings in the web.config file. If these keys were in the web.config file, the settings shown on the portal would take precedence.