Are there any limitations or considerations when it comes to payment gateways for multiple stores on Shopify?

Apart from being aware of payment gateway transaction fees, and ensuring the gateway you want to use is compatible with Shopify, you should keep in mind that when you share a payment gateway between multiple stores, it also shares the same settings and configurations.

If you want your payment gateways to be set up differently, you will need to set up separate gateways.

You will also want to take note of the countries that your gateways are available in. If you are sharing a payment gateway between multiple stores that are targeted at different countries, you may run into a payment problem if the payment gateway isn't supported in one or more of the countries.