AWS provides guidelines as to how to upgrade a MySQL 5.5 instance to MySQL 5.6 using read replicas. However, its final step is to point your application to the new database, but EBS provides no mechanism through the web console to point your application to a different database. What is the recommended path to upgrading EBS-based RDS instances?
To upgrade an MySQL database while a DB instance is in useSign in to the AWS Management Console and open the Amazon RDS console at https://console.aws.amazon.com/rds/ . Create a read replica of your MySQL 5.7 DB instance. This process creates an upgradable copy of your database.
You can upgrade your instances by using the RDS console or the AWS CLI command modify-db-instance. You can also upgrade instances to suitable minor versions by enabling Auto Minor Version Upgrades.
I generally advise users to provision the Database outside of Beanstalk, this issue being one of them.
Also
For a production environment, you may want to launch a database instance outside of your environment and configure your application to connect to it outside of the functionality provided by Elastic Beanstalk.
AWS RDS does support the 5.5 to 5.6 upgrade.
MySQL 5.5 to MySQL 5.6
https://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/USER_UpgradeDBInstance.MySQL.html
But in your current setup.
In the Environment Properties section, define the variables that your application reads to construct a connection string. For compatibility with environments that have an integrated RDS DB instance, use the following:
RDS_HOSTNAME – The hostname of the DB instance.
Amazon RDS console label – Endpoint is the hostname.
RDS_PORT – The port on which the DB instance accepts connections. The default value varies between DB engines.
. Amazon RDS console label – Port
RDS_DB_NAME – The database name, ebdb.
Amazon RDS console label – DB Name
RDS_USERNAME – The user name that you configured for your database.
Amazon RDS console label – Username
RDS_PASSWORD – The password that you configured for your database.
https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/AWSHowTo.RDS.html
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