Onboarding workers to payroll

Last updated: September 24, 2026

A worker who has not finished payroll onboarding is not paid — even if they worked all period and signed every note. This article is the admin's guide to getting your team onboarded and spotting the ones who have stalled.

What onboarding involves

Each worker has to complete their own payroll setup: tax withholding information and direct deposit / banking details. Only the worker can do this — you cannot enter their bank details for them. Until they finish, they are not payment-ready and the payroll run will skip them.

The admin's part

Add the team member via Invite Team Member, filling in the Employment step (worker type (W-2 or 1099-NEC), start date, compensation structure) and the Compensation step (rates). This creates their payroll contract.
The worker receives an invite and completes their own tax and banking setup from My Payroll → Profile.
Track who is still outstanding on Payroll → Onboard Workers.

See W-2 employees vs 1099-NEC contractors for the classification decision, and Worker rates and when to edit them for the rates.

Spotting the ones who will be missed

The homepage warns you before the deadline, not after the run.

In the run-up to each payroll deadline, the Needs your attention card on your homepage adds a line like "2 workers with pay this period not onboarded to payroll yet". It only counts workers who actually have hours in the period, so it does not fire on dormant accounts — if it appears, those are real people about to miss a paycheck.

Chase them before the period closes. A worker onboarded after the deadline is paid in the following period, not retroactively in the one they missed.

The organization also has to be set up

The setup-task banner at the top of Payroll Details.

Alongside per-worker onboarding, your organization has its own payroll setup. Two places to watch:

Payroll → Onboarding — the guided employer setup: bank account, signatory, tax info, work locations and workers.
The setup-task banner at the top of Payroll Details — it lists any outstanding tasks by name, with a Go to Onboarding link.

One task, Sign company documents, has no home in the Onboarding flow, so Alpaca surfaces a Sign company documents button directly on that banner. Clicking it opens the signing experience in place.

Your state tax registrations are tracked separately — see The Expected Tax Notices tab.

Common reasons a worker stays "not ready"

They have not opened their invite, or it went to a work email they do not check.
They started the flow and stopped before entering bank details.
Their tax information is incomplete for the state they work in.
They were added without a payroll contract — check that the worker type and hire date are set on their Pay Rates card.

Payroll setup & migration checklist — bringing an existing practice onto Alpaca Payroll
Who gets payroll?
The Expected Tax Notices tab
Operating in Multiple States: Foreign Qualification & State Payroll Tax

Still stuck? Email support@alpacahealth.io and we will take a look.