To run payroll in QuickBooks Desktop, set up a payroll schedule (Employees > Add or Edit Payroll Schedules), then go to Employees > Pay Employees, select the schedule, enter hours, review each paycheck, and create them — printing checks or sending direct deposit. Afterwards, pay your payroll taxes under Employees > Payroll Taxes and Liabilities > Pay Scheduled Liabilities.
It's payday. Your team did the work, and now the money has to move — correctly, on time, with the right taxes withheld. If you've never run payroll in QuickBooks Desktop before, the process can look intimidating: schedules, liabilities, tax tables, direct deposit cutoffs.
Here's the good news: once it's set up, running payroll is mostly a rhythm — enter hours, review, create, send. This guide walks you through the whole thing, including the two parts people forget (tax tables and liabilities). Let's go.
One common confusion to clear up first: QuickBooks Desktop payroll requires an active payroll subscription. The accounting software alone doesn't include payroll — you need a payroll service (Basic, Enhanced, or Assisted) with a valid payroll service key. No key, no payroll. We'll cover that below.
Before you start: get these in place
1. An active payroll subscription and service key.
If you haven't entered your payroll service key yet, do that first — here's [how to enter your payroll service key in QuickBooks](/enter-payroll-service-key-in-quickbooks/). Without it, the payroll menus won't fully work.
2. Employee records, complete and current.
Every employee needs to be set up in the Employee Center with their W-4 info, pay rate, pay frequency, and (for direct deposit) bank account details. Garbage in, garbage out — paychecks are only as right as the employee records behind them.
3. Updated payroll tax tables.
QuickBooks downloads the latest federal and state tax tables with your payroll subscription. Before every payroll run, make sure they're current: Employees > Get Payroll Updates, then Download Entire Update. Tax rates change; running payroll on stale tables means wrong withholdings.
How to run payroll, step by step
Step 1: Set up a payroll schedule
Payroll schedules group employees by pay frequency so you can pay them as a batch.
- Go to Employees > Add or Edit Payroll Schedules.
- Click New and give the schedule a name (like "Biweekly – Salaried").
- Choose the pay frequency: Weekly, Biweekly, Semimonthly, or Monthly.
- Set the pay period end date and the paycheck date.
- Assign your employees to the schedule. Click OK.
- Most businesses need just one or two schedules (e.g., one for salaried, one for hourly). Keep it simple.
Step 2: Start a payroll run
- Go to Employees > Pay Employees.
- Select the payroll schedule you want to pay, and confirm the pay period dates and paycheck date. Double-check these — wrong dates are one of the most common payroll mistakes.
- Click Start Scheduled Payroll.
Step 3: Enter hours and review
- For hourly employees, enter their hours. If you've been tracking time in QuickBooks, those hours can flow in automatically — review them either way.
- For salaried employees, confirm the salary amounts look right.
- Check each employee's row: pay rate, hours, deductions, and any one-off additions (bonuses, reimbursements).
- Click Continue, and QuickBooks calculates gross pay, taxes, and deductions for every paycheck.
Step 4: Review every paycheck
Don't skip this. QuickBooks shows you a summary of each paycheck before anything is created.
- Look at gross pay, tax withholdings, and net pay for each employee.
- Spot-check one or two against what you expect. Something off by a little is usually a wrong hour count; something off by a lot is usually a wrong pay rate or date.
- Fix anything now — it's far easier than fixing a paycheck after it's created.
Step 5: Create the paychecks
- Choose your payment method: print paychecks (QuickBooks prints them on check stock) or direct deposit.
- For direct deposit: select the employees, and click Send Payroll Data to transmit it to Intuit. Watch the cutoff time — direct deposit needs to be sent by 5:00 PM Pacific, two business days before the paycheck date (timing varies by plan, so confirm yours).
- For printed checks: load your check stock, print, and have them signed.
- QuickBooks records every paycheck in your books automatically — payroll expenses, tax liabilities, the works.
Step 6: Pay your payroll liabilities
Running payroll creates tax liabilities — the withheld taxes and employer contributions you now owe. Paying employees is only half the job; paying the agencies is the other half.
- Go to Employees > Payroll Taxes and Liabilities > Pay Scheduled Liabilities.
- Select the liabilities due (federal 941, state withholding, unemployment, etc.) and the correct period.
- Review the amounts, choose View/Pay, and create the payment — by check or e-payment.
- Miss this step and the liabilities just sit there accumulating. If your liability balances ever look wrong, here's how to [zero out payroll liabilities in QuickBooks](/zero-out-payroll-liabilities-in-quickbooks/).
Common mistakes to avoid
- Running payroll on outdated tax tables. Always download payroll updates before a run. Stale tables = wrong withholdings = a mess at quarter-end.
- Wrong pay period or paycheck dates. This throws off reports, tax filings, and employee pay stubs. Confirm the dates on the Start Payroll screen every single time.
- Missing the direct deposit cutoff. Send payroll data late and your team gets paid late. Know your plan's cutoff and set a personal deadline a day earlier.
- Forgetting payroll liabilities. The paychecks are done, everyone's happy — and the tax payments sit unpaid. Build liability payments into your payroll routine, not as an afterthought.
- Not reviewing before creating. QuickBooks calculates; you verify. The review screen exists for a reason — use it.
Conclusion!
That brings us to the end of this guide on running payroll in QuickBooks Desktop. We hope the steps explained above helped you process paychecks confidently — from schedules to direct deposit to those easy-to-forget tax liabilities. If you run into any difficulty while following the steps, consider consulting a qualified and experienced QuickBooks professional for further assistance.
FAQs
Do I need a payroll subscription to run payroll in QuickBooks Desktop?
Yes. QuickBooks Desktop alone doesn't include payroll processing — you need an active payroll subscription (Basic, Enhanced, or Assisted) and a valid payroll service key entered in the software.
Can I run payroll for just one employee outside the schedule?
Yes. Use Employees > Pay Employees > Unscheduled Payroll for off-cycle payments like bonuses, corrections, or termination pay.
What’s the difference between the pay period end date and the paycheck date?
The pay period end date is the last day of work covered by the paycheck. The paycheck date is when employees actually get paid. They're different dates, and getting them mixed up is a classic mistake.
How do I fix a paycheck after it’s been created?
Void or delete the paycheck and recreate it — but only before it's been sent or cashed. For direct deposit paychecks that already transmitted, you'll need to handle it as an adjustment in the next payroll. When in doubt, fix it in the current period rather than editing history.
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