If you’re not using QuickBooks’ software already – or you don’t want to – there really aren’t many reasons to choose QuickBooks Payments. Sure, you generally lower transaction rates, but Square offers more payments tools and POS features at no monthly cost.
If you want a payment platform that has all the software features needed to run a business, Square caters to it all. If something is missing, you can probably connect to an external system that provides those tools.
If you do use QuickBooks for accounting, QuickBooks Payments would keep all transactions together in one account, but the GoPayment app is only for simple in-person transactions (not complicated retail inventory, for example). You get a full merchant account with a lower risk of account holds, and ACH payments, which Square doesn’t offer.
Retailers, restaurants or other face-to-face businesses will probably prefer Square for its user-friendly POS systems for any industry. The QuickBooks Point of Sale software isn’t great, but then again, you can integrate QuickBooks accounting with many point of sale systems.