Run payroll step by step in Payroll Calculator

Product guide · Last reviewed May 30, 2026: Run a pay period in Payroll Calculator. Confirm amounts before paying employees outside the app.

Before you run

• Company profile complete (setup guide)
• At least one active W-2 employee (employee guide)
• You know the pay period dates and gross pay (or hours) for each person

Payroll Calculator calculates taxes and net pay—it does not move money to employee bank accounts.

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Step 1 — Open Run payroll

1. Go to Workforce (/workforce).
2. Select the Run payroll tab.

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Step 2 — Choose pay period

1. Use month shortcuts or pick start/end dates for the period.
2. The app uses year-to-date (YTD) totals from prior runs in the same calendar year for wage caps and additional Medicare.

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Step 3 — Select employees

1. Check each W-2 employee you are paying this period.
2. 1099 contractors do not appear in pay runs—skip them here.
3. Inactive employees are excluded.

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Step 4 — Per-employee overrides (optional)

For this run only, you can override:

Defaults come from the employee record.

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Step 5 — Owner health insurance checklist

If you marked owners on company profile and employees:

1. Read the health insurance checklist panel on the run page.
2. Confirm premiums are handled per your entity type (Box 1 wages; optional FICA exclusion for typical S-corp >2% owners).
3. Use ClearLedger reconciliation panel if you sync books—labels must match your CPA plan.

Not modeled: Pre-tax Section 125 qualified plan deductions in this checklist.

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Step 6 — Run payroll

1. Click Run payroll for selected.
2. Wait for the API to compute taxes (FIT, FICA, state taxes for CA or WA).
3. Review each row: gross, taxes, net, employer cost.

If something looks wrong, do not pay employees yet—edit employee withholding or company rates, then re-run or use history edit (see history guide).

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Step 7 — CSV bulk run (paid license)

1. Export CSV template from the run page.
2. Fill one row per employee/period with pay and hours.
3. Import and run in bulk.

Same tax engine as single run. Requires import-enabled license.

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Step 8 — Pay employees (outside the app)

1. Use net pay amounts from the run to pay via your bank or payroll service.
2. Set aside withheld taxes and employer taxes for deposits per IRS/EDD/WA rules.
3. Payroll Calculator does not remit taxes for you.

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Step 9 — Confirm on Dashboard & Reports

1. Dashboard — gross and employer cost should update.
2. Reports — 941 and DE-88 lines accumulate by pay date (see tax reports guide).

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Common issues

Next: Payroll history, edits, and exports