Payroll setup & migration checklist

Last updated: July 28, 2026

This is the at-a-glance checklist for getting your practice's payroll fully live in Alpaca — whether you're brand new or moving from another payroll provider mid-year. It ties together the detailed setup articles into one runnable list so nothing gets missed, with special attention to the parts that trip up practices migrating an existing payroll.

For the step-by-step on each item, see "Set Up Your Organization Payroll Account," "Registering your state payroll tax accounts," and "Set Up Individual Employee Payroll."

Before you start — gather these

A few items depend on outside agencies and take time to obtain, so collect everything up front:

Your EIN
Signatory details — the person authorized to sign payroll and tax forms
Filing and mailing addresses for the business (tracked separately)
Company bank routing and account numbers (the funding account)
State withholding and unemployment (UI) account numbers and rates for every state you employ in
Work location address(es) — where staff physically work
Your intended pay schedule
Prior payroll history — required if you've already run payroll this year (see the migration section)

The organization setup checklist

Open Payroll from the sidebar, go to the Onboarding tab, and work the guided wizard. Alpaca tracks what's outstanding as setup tasks, with a badge on the Payroll Dashboard counting anything left. You're payroll-ready when no setup tasks remain.

Step	Notes
☐ Complete signatory information	The authorized signer for payroll and tax forms.
☐ Add filing and mailing addresses	Both are tracked separately — don't leave one blank.
☐ Add company bank account	The account payroll is drawn from.
☐ Verify the bank account	A separate step (micro-deposits or instant verification). It can't fund payroll until verified.
☐ Complete employer tax setup	EIN plus state withholding + UI numbers and rates for each state. Usually the longest step. See "Registering your state payroll tax accounts," plus the State Tax Guides and Expected Tax Notices tabs.
☐ Add at least one work location	Drives which state's taxes apply — use where staff actually work, not a home address entered by mistake.
☐ Set up workers + a recurring pay schedule	Add workers and create the pay group payroll runs on.
☐ Complete prior payroll history	Required if you ran payroll earlier this year (see below). New businesses move past this quickly.

Migrating from another payroll provider

If your practice already ran payroll this year, a few extra things matter so year-to-date totals and taxes stay correct:

Declare and load prior payroll history. In the wizard's prior-payroll step, provide or import the year-to-date history. This keeps YTD wages, taxes, and caps (like Social Security wage base) accurate so employees aren't over- or under-withheld.
Reuse your existing state tax account numbers. If you were already paying employees in a state, you already have withholding/UI accounts — enter those numbers and current rates rather than registering new ones.
Pick a clean cutover date. Migrating at the start of a quarter is simplest for reconciling filings. Confirm which provider is responsible for the final filings of the prior period so nothing is double-filed or missed.
Carry over leave balances. Use Manual Leave Time Entry to set each employee's starting PTO/leave balance. See "Set Up Leave Time" and "PTO & leave: accruals + the Leave Time tab."
Re-confirm each employee's setup. Direct deposit and tax withholding elections don't automatically transfer — see "Set Up Individual Employee Payroll."

Common stalls

Symptom	Fix
Setup won't complete	A task is still outstanding — the Onboarding tab lists it with a shortcut to finish it.
Waiting on a state number	Expected — states issue these on their own timeline. See "Registering your state payroll tax accounts" and the state setup guides.
Outstanding-tasks badge disappears then returns	Expected during a routine sync — you haven't lost progress.
Unexpected state tax requirement	See "Resolving Unexpected State Tax Requirements During Payroll Setup."

Employing staff in more than one state? Also see "Operating in Multiple States: Foreign Qualification & State Payroll Tax." For anything you can't clear, contact support@alpacahealth.io.