European Consumer Organisation (BEUC), the Norwegian Consumer Council and the Transatlantic Consumer Dialogue took their grievances to the EU executive in April last year.
They said users had to go through numerous hurdles such as complicated navigation menus, skewed wording and confusing choices, to unsubscribe from Amazon Prime.
The company will now allow users to unsubscribe from Amazon Prime with two clicks via a prominent and clear 'cancel button', the Commission said.
The changes will apply to all EU websites and for desktop devices, mobiles and tablets with immediate effect.
"Consumers must be able to exercise their rights without any pressure from platforms. One thing is clear: manipulative design or 'dark patterns' must be banned," Justice Commissioner Didier Reynders said in a statement.
(Reporting by Foo Yun Chee; editing by Jason Neely)
By Foo Yun Chee