How do I run payroll for more than one EIN?

operatordirectorLast verified Oct 5, 2026

If your organization pays people from more than one business, add each EIN on the Organization page. Each EIN is its own company with its own bank and its own Company setup. Use the EIN dropdown at the top to switch between them, and set Paid by on each person.

Where:

Payroll → Organization, at the top of the page.

Add an EIN

Click + Add an EIN at the top of the page and name it. If you already have EINs, use + Add EIN in the EIN dropdown. If you only have one EIN, skip this.

Set up each EIN

Company setup runs for each EIN on its own, not for your organization as a whole. Pick the EIN in the dropdown, then complete 1. Company setup. See PR-03.
Each EIN has its own bank, so you confirm the bank deposits for each one. See PR-05.
Each EIN has its own Payments card showing whether it's ready to pay. See PR-12.
Your pay schedule applies to all your EINs.

Assign people to an EIN

On Employees & Contractors, each row has a Paid by dropdown. When you upload a spreadsheet, pick the EIN at the top of the page first, and everyone in the file is assigned to it. See PR-06.

Good to know

If you can view an EIN's payroll but aren't an approver for it, you'll see "You can view this payroll but you are not an approver for this EIN, so approving is disabled." See PR-03 for approvers.
On Reports, you can export one EIN or All EINs. See PR-14.
State new-hire reports for contractors are filed under each paying EIN. See PR-15.