Securing your instances in what way? Elastic Beanstalk should initially provide you with instances that one would expect to be reasonably secure, but I wouldn't rely on that level of presumed security for anything important. It definitely does not provide a fully managed environment on an ongoing basis. One glaring example is that it does not handle things like OS-level security updates/patches, or provide you with instances running updated AMIs unless you re-setup your EB environment.