Billing by Shopify or bill outside of Shopify app, what should we do?

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We collect charitable donations on customer orders by our webapp at checkout. We charge a subscription on our webapp for our software and then an extra fee on top of the donations like a small credit card charge. The install will soon be by Shopify app which we are building. 

We can't give any of the donation money to Shopify so paying something like 20% Shopify Marketplace store fees is impossible. 

Do we keep all billing outside of the Shopify app and only have the app for free to install.

Or should we bill using Shopify billing system?


Any advice on what is best way forward would be really helpful?







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