AWS Elastic Beanstalk - how to run php and nodejs in same ec2 instance

I'm using Elastic Beanstalk to deploy a root app (node.js) and also want to run php code that node.js app needs to call in the same ec2 instance.

When I connect to the instance it says:

This EC2 instance is managed by AWS Elastic Beanstalk. Changes made via SSH WILL BE LOST if the instance is replaced by auto-scaling. [...]

It means that when I add php sources in /var/www/ folder (connected via ssh), it will be removed if the instance changes.

how could I run in the same instance node.js and php ?