How to encrypt web.config section AND deploy to multiple servers with Amazon Elastic Beanstalk

Following @kukido 's suggestion what you need to do is create an .ebextension file with the following content.

commands:
  encryptConfig:
    command: aspnet_regiis.exe -pe "connectionStrings" -app /
    cwd: %windir%\\Microsoft.NET\\Framework64\\v4.0.30319

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