Elastic Beanstalk will only modify the instances, autoscaling groups it creates as part of environment creation. If you already have instances running in your account they should not be affected by simply using Elastic Beanstalk to launch new instances.
Make sure you do not share those resources with your new environment. e.g. If you have an existing RDS and you access that RDS from your application on the newly launched instances by beanstalk, then it goes without saying that the state of the RDS can be modified by your application. Likewise if you use preexisting security groups then you are sharing state between your existing resources and your beanstalk environment and should be avoided.
But just launching a new beanstalk environment, deploying your application there will keep the existing instances in your account untouched.