3.1 Set Up Your Organization Payroll Account

Last updated: July 23, 2026

This is the one-time, organization-level setup that lets your practice run payroll. An owner or admin completes it once, and it's what makes every future payroll run file and pay correctly. Alpaca walks you through it as a guided onboarding wizard; you finish each step, and Alpaca tracks what's still outstanding for you.

Where to Go

  1. Log into Alpaca and open Payroll from the sidebar.

  2. Open the Onboarding tab.

  3. Work through each step the wizard presents.

Alpaca shows what's left as a set of setup tasks, and a badge on the Payroll Dashboard tab counts anything still outstanding. When no setup tasks remain, your organization is payroll-ready.

What You'll Complete

The wizard guides you through the following. Have the information for each ready before you start, since a couple of these depend on outside agencies and can take time.

  • Complete your signatory information. The authorized person who signs payroll and tax forms for the business.

  • Add your filing and mailing addresses. Both are tracked separately, so don't leave one blank.

  • Add your company bank account. The funding account (routing and account number) payroll is drawn from.

  • Verify your bank account. This is a separate step from adding it. Verification usually happens by micro-deposits or instant verification, and the account isn't usable for payroll until it's verified.

  • Complete your employer tax setup. Your EIN plus the state withholding and unemployment (UI) account numbers and rates for each state where you employ staff. This is usually the longest step, because states have to issue those numbers first. See 3.2 Registering your state payroll tax accounts for how to get them, and use the State Tax Guides and Expected Tax Notices tabs to see exactly what each state needs.

  • Add at least one work location. Where your employees physically work. Work location drives which state's taxes apply, so set it to where staff actually work, not a home address entered by mistake.

  • Set up your workers and a recurring pay schedule. Add your workers and create the recurring pay schedule (pay group) payroll runs on.

  • Complete your prior payroll history. If your business already ran payroll earlier this year, declare it here and provide or import that history so year-to-date totals are correct. New businesses that haven't run payroll can move past this quickly.

How You Know You're Done

You're payroll-ready when no setup tasks remain. Until then, each outstanding item shows up as a task, with a shortcut back into the Onboarding tab to finish it. If the outstanding-tasks badge briefly disappears and returns, that's expected during a routine sync and doesn't mean you lost progress.

Have These Ready (Checklist)

  • Your EIN

  • Signatory details (the person authorized to sign)

  • Filing and mailing addresses for the business

  • Company bank routing and account numbers

  • State withholding and UI account numbers and rates for each state you employ in (see 3.2)

  • Work location address(es)

  • Your intended pay schedule (how often you pay)

  • Prior payroll history, if you've already run payroll this year

Common Stalls, and How to Avoid Them

  • Adding a bank account is not the same as verifying it. "Verify your bank account" stays outstanding until verification completes, so start it early and don't assume you're done once the account is added.

  • Tax setup is the biggest blocker, and it's agency-paced. You can't finish it until the states issue your withholding and UI numbers, so start state registration as early as possible (3.2). It carries a longer timeline and is never auto-flagged as overdue for this reason.

  • A work location is required. Payroll can't be set up without at least one.

  • Don't skip the recurring pay schedule. Payroll readiness needs it.

  • Answer the prior payroll history question if it applies to you; leaving it pending blocks readiness.

  • After you enter state tax numbers in the wizard, give them up to a minute to reflect elsewhere in Alpaca.

Stuck on any step, or something isn't updating? Email support@alpacahealth.io and we'll help you finish setup.