If you plan to use your own VPC (with private Subnet), the configuration is tricky. you have to configure it on the .ebextensions files. Never use the --sample as the project contains is own ebextensions entering into conflict with yours (trying desesperatly to deploy on the default vpc) If your projet is based on git repo and you process a compile step (composer, nodes, yarn or whatever), with eb deploy command, only the files existin into the repo are deployed and uploaded into the instance. The tricks? Setup a .ebignore (empty if you want everything, but better to put node package out) @TO DO to be reshaped