We have a nationwide contract with the federal government that requires us to pay certain labor categories a w2 only. 1099 is not allowed. QuickBooks Online is our accounting system but doesn't support U.S. territories like Guam or Puerto Rico. There has to be an add-on or work around for employees who reside in Puerto Rico. We cannot be the only firm with this issue.
Let me share the QuickBooks Online International versions that don't have payroll built-in feature. For now, we only offer payroll service to the following countries:
You may consider looking for a third-party app that can integrate with the system. I'm also taking note of this suggestion and send this preference to our developers so they might consider adding this feature for future updates.
In addition, you can visit our QuickBooks Blog regularly. From there, you'll be updated with the features and enhancements that our developers are currently working on.
If there's anything else I can do to help, I'm just a post away.