Any payments or checkout functionality that you build into your website will continue to work within your GoNative apps.
For Android, you may continue to use your web-based payments flow in your apps without any issues.
Apple, however, makes a distinction between "physical" and "digital" goods sold within your app, and requires use of their in-app purchase ("IAP") APIs for selling "digital" goods so that they can take their 30% cut.
A "physical" good is something delivered or consumed outside of your app. For example, the Amazon.com app sells physical goods and thus does not need to use Apple's in-app purchase APIs. These purchases can go through standard web checkout flow like Stripe, PayPal, etc.
A "digital" good is something like a new weapon in a game, or a workout video delivered as part of a premium membership in your app. Digital goods are delivered or consumed within your app, and payments are required to go through Apple's in-app purchase APIs.
There are two main strategies to tackle this problem:
1. Remove ability for people to make digital purchases, or make your app a "members-only" app. People can use your app like normal, but simply cannot make digital purchases within it.
If you are looking to make small modifications to your website to remove these payment links, please see our guide at http://support.gonative.io/knowledge_base/topics/how-do-i-detect-usage-coming-from-my-apps
2. Hire us to implement Apple's in-app purchase APIs in your app. This requires some additional logic on your website so that you can still control the process, as well as a good amount of native development on our side. If you are interested, please contact us describing your requirements and we will get back to you with more information and pricing.