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The correct payroll workflow depends on your QuickBooks product. In QuickBooks Online Payroll, go to All apps → Payroll → Employees → Run payroll, confirm the pay schedule and dates, enter or approve pay details, preview the totals, verify the funding account, and select Submit payroll. QuickBooks Desktop Payroll uses a separate Payroll Center workflow and may leave tax payments and filings to you. Use the matching section below.
This guide assumes a U.S. employer. Federal, state and local rules, deadlines and product features vary by jurisdiction and subscription.
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Before you process payroll
Payroll setup is the compliance foundation. Complete these checks before opening a pay run.
Confirm the product and payroll service
- For Online, check Settings → Subscriptions and billing and identify whether your account uses QuickBooks Online Payroll/Core, Premium or Elite. Some screens use the name Intuit QuickBooks Workforce.
- For Desktop, open Employees → Payroll Center → Payroll to see the payroll service. Desktop Payroll Basic and Standard are no longer offered in current Intuit documentation; affected users may be moved to Enhanced Payroll. See Intuit’s payroll-service guidance.
- Ensure you have payroll-admin permissions and an active subscription.
Verify company, bank and tax setup
- Legal business name, address and federal Employer Identification Number
- State employer accounts and applicable local registrations
- Payroll bank account, bank verification and direct-deposit authorization
- Tax-payment and electronic-filing authorizations
- Federal, state and local tax rates, account numbers, deposit frequencies and effective dates
- Correct accounting and fiscal-period settings
Deposit frequency comes from the relevant tax agency, not simply from a QuickBooks setting. Direct deposit also requires bank verification, funding and submission before the applicable cutoff.
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Review every employee record
- Legal name, address and Social Security number
- Federal and state withholding forms and tax jurisdictions
- Hourly, salary, commission or other pay type and current rate
- Pay schedule, work locations and employment status
- Deductions, benefits, garnishments and paid-time-off balances
- Direct-deposit instructions
- Hire date and active status
An employee generally must be active for at least part of the pay period to appear in a scheduled Online payroll. If someone is missing, check status, hire date, schedule and setup; do not create a duplicate profile.
Enter prior payroll when starting or switching midyear
If employees were paid earlier in the calendar year, enter prior wages, taxes and tax payments before running new payroll. Use pay stubs or payroll reports to provide each paycheck date, wage and tax totals, current-quarter company totals, and prior filings or payments. Profiles alone do not create accurate year-to-date totals for quarterly and year-end forms. Intuit’s setup instructions are at Get started with QuickBooks Online Payroll and enter prior payroll.
Approve time
- Import or enter hours and approve timecards.
- Check overtime, double time, holiday, sick and vacation hours.
- Confirm job, class and location coding.
- If you use QuickBooks Time, make sure approved entries will not be imported twice.
How to process payroll in QuickBooks Online
- Open the payroll workspace. Select All apps → Payroll → Employees, or the Payroll item in the left navigation, then choose Run payroll. Labels can vary by interface and subscription.
- Choose the pay schedule and dates. Select weekly, biweekly, semimonthly or monthly payroll. Confirm the pay-period start date, end date and pay date. The pay date controls employee expectations, tax liability timing and direct-deposit scheduling.
- Select employees. Check for omitted new hires, future-start employees, former employees accidentally included, rate changes and multiple work locations.
- Enter or review pay details. Open an employee row or choose Actions → Edit paycheck. Review regular, overtime and double-time hours; salary; commissions; bonuses; reimbursements; tips; paid time off; deductions; benefits; garnishments; memo notes; and class, location or customer/job coding.
- Review approved time. With QuickBooks Time, select Review Approved Time. Confirm the employee, pay-period dates, overtime treatment and job coding, and ensure previously paid hours are not imported again.
- Preview payroll. Select Preview payroll and inspect gross wages, employee and employer taxes, deductions, net pay, direct-deposit and printed-check amounts, payroll liabilities, cash required and unusual changes from the prior run.
- Verify the bank account. Confirm the correct company account, available cash, connection and verification status. Understand when direct-deposit and tax withdrawals will occur.
- Submit. Select Preview payroll details, then Submit payroll. For an unscheduled run, you may be able to choose Save for later. Submission sends the payroll for processing; delivery remains subject to cutoff, funding, banking and holiday conditions. See the current Online payroll instructions.
- Save the record. Save or print the confirmation, make pay stubs available, review payroll liabilities and tax status, and reconcile bank activity after transactions clear.
How to run a bonus, commission or final paycheck
Use an unscheduled payroll for a bonus, commission, fringe benefit, final paycheck or supported special adjustment. In Online Payroll:
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- Open Run payroll and use the dropdown.
- Choose Bonus only, Commission only or Fringe benefits only.
- Answer the additional tax or calculation questions.
- Set the pay period and pay date if requested, select employees and edit paycheck details.
- Select Preview payroll, verify the bank account, then select Preview payroll details.
- Choose Submit payroll or Save for later, then select Close.
Supplemental wages can have different federal and state withholding treatment from ordinary wages. Check year-to-date totals and applicable rules rather than assuming the regular paycheck calculation applies.
Checks to complete before submitting
| Check | Why it matters |
|---|---|
| Pay period and pay date | Prevents a misdated or late payroll and places liabilities in the correct period. |
| Employee list | Catches omissions, duplicate profiles and terminated employees. |
| Hours and overtime | Prevents wage errors and incorrect overtime taxation. |
| Rates and salary | Captures recent raises, schedule changes and new-hire rates. |
| Deductions and benefits | Prevents incorrect net pay and benefit balances. |
| Taxes and jurisdictions | Exposes setup, rate, address or work-location problems. |
| Bank account and cash | Reduces failed withdrawals and overdrafts. |
| Direct-deposit cutoff | Protects the stated payday; weekends, holidays, verification and funding can change delivery. |
What happens after you submit payroll
Employee payments and pay stubs
Depending on setup, employees receive direct deposit, a printed check, a QuickBooks Workforce pay stub or a combination. Do not promise same-day or next-day delivery without confirming the plan, cutoff, bank conditions and funding status. QuickBooks advertises different speeds by product and offer at its Workforce Payroll page.
Tax liabilities, deposits and filings
A payroll can create federal income-tax withholding, Social Security, Medicare, FUTA, state withholding, state unemployment, paid-leave or disability and local liabilities. QuickBooks may calculate and, depending on product and setup, pay and file some of them. Coverage is not universal: local-tax support varies by plan, and certain taxes such as New York SDI and Hawaii TDI may require separate handling. Review the plan-specific list in Intuit’s tax-payment and form coverage.
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Potential filings include Forms 941 or 944, Form 940, Form 943 where applicable, W-2/W-3, state withholding and unemployment forms, new-hire reports and some local forms. Agencies process payments at different speeds, and Intuit warns that money may need to be submitted several business days before the official due date. Follow the status in Pay and file payroll taxes and forms.
Automated-tax behavior for applicable Online Payroll customers changed on July 1, 2026, according to Intuit’s setup guidance. Confirm your account’s authorizations and effective date instead of assuming automation is active.
Reports and reconciliation
In Reports, review Payroll Summary, Payroll Tax and Wage Summary, Payroll Tax Liability, Total Payroll Cost, payroll history, tax payments, tax forms, employee earnings and paid-time-off reports. Match payroll funding and tax withdrawals to the bank account and reconcile them when they clear.
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- Payroll Record Book for Small Busines：This payroll record book is designed for small business owners contractors and offices to easily track employee payroll information helping simplify bookkeeping and payroll management
- Weekly and Daily Time Sheet Log Book for One Year：Designed as a weekly payroll record book and daily time sheet log book it tracks weekly hours pay rates taxes and deductions for up to 52 weeks providing full year employee payroll and time tracking in one book
- Large 8.5 x 11 Inches with 106 Pages：The payroll record book measures 8.5 x 11 inches with 106 pages offering ample space for detailed payroll records employee time tracking and work hours logs without overcrowding
- Tracks Payroll for Up to 20 Employees：This employee payroll record book and work hours log allows recording payroll data for up to 20 employees with clear columns making it suitable as an employee time tracking book for small teams
- Eye Friendly Design with Durable Spiral Binding：Blue green inner pages reduce eye strain during long bookkeeping sessions while the horizontal spiral bound design and laminated cover ensure durability and easy flat writing for daily payroll and time sheet logging
QuickBooks Desktop Payroll
Do not apply the Online menu path to Desktop. The service level matters: Enhanced Payroll can require the employer to pay and file liabilities, while Assisted Payroll provides a different level of Intuit handling. Employers remain responsible for checking that payments and filings were accepted.
The current Desktop workflow generally uses Employees → Payroll Center: select the scheduled payroll, confirm pay-period dates and pay date, open paycheck detail for each employee, enter hours or salary and additions and deductions, review taxes and net pay, create or submit paychecks, process direct deposit if enabled, and then review and pay liabilities and forms through the applicable service. Because screens and options vary by Desktop edition and release, verify the exact instructions for your service before submitting. Intuit’s current product distinctions are summarized in its Desktop payroll guidance.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.How to correct a payroll mistake
Before submission
Edit the paycheck, correct hours, rates, deductions or setup, preview again and verify the revised cash requirement. Investigate the configuration that produced an unexpected tax instead of casually overriding the amount.
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- Includes pages to record payroll by weeks and quarterly
- Pages to record Depository Payments by Month
- Pages to record yearly totals up to 50 employees
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After submission but before payday
The remedy depends on processing status, direct-deposit transmission, printed checks and whether tax withdrawals or filings have started. Contact QuickBooks Payroll support promptly. Do not delete transactions or create an unexplained offsetting paycheck.
After payday or after filing
Possible remedies include a next-payroll correction, an off-cycle adjustment, a permitted void or replacement, a liability adjustment, an amended tax form or a corrected W-2. Coordinate with a payroll accountant when a filed return or year-end form is affected; changing a historical paycheck can alter reported liabilities.
Common cases
- Wrong hours: Determine whether the employee was underpaid or overpaid, preserve an audit trail and pay wages owed promptly.
- Wrong withholding: Check employee setup, jurisdiction, rate, benefit treatment and service calculation before correcting.
- Wrong bank account: Establish whether submission, direct-deposit transmission or withdrawal has occurred and contact support and the bank immediately.
- Employee omitted: Use an off-cycle payroll or supported correction process; never create a duplicate profile.
- Employee paid twice: Contact payroll support and the bank. Any repayment or deduction agreement must comply with applicable wage law.
- Rejected tax payment: Identify the rejection, correct bank or agency information and determine whether a manual payment is needed before the deadline. Intuit’s terms state that employers remain responsible for ensuring transactions are sent, received and accepted: Desktop Payroll terms.
Is QuickBooks Payroll the right fit?
QuickBooks is usually a good fit for a small or moderately sized employer already using QuickBooks accounting that wants integrated payroll calculations, employee pay information, reports and an available full-service tax option. It may be a poor fit for extensive multi-state or local taxation, union rules, unusual wage calculations, complex garnishments, international workers, frequent payroll-history migrations or a need for dedicated compliance support.
Gusto (product page) and Patriot (pricing page) are dedicated small-business alternatives. ADP (products) and Paychex (payroll) are more oriented to broader payroll, HR and scaling support. A local payroll accountant or bureau is often the safest choice for unusual, multi-state or compliance-heavy payroll. Feature availability and prices change; compare current offers directly.
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Reusable payroll-run checklist
- Confirm the correct Online or Desktop service and administrator access.
- Verify company, bank, tax-account and filing authorizations.
- Enter prior payroll history when starting midyear.
- Approve hours, overtime, leave and job coding.
- Check employee status, pay rates, deductions, benefits and tax jurisdictions.
- Confirm pay-period dates, pay date and direct-deposit cutoff.
- Compare preview totals with the prior payroll and expected headcount.
- Verify bank funding, employee net pay and tax liabilities.
- Submit only after the preview is reconciled.
- Save confirmation, provide pay stubs, monitor payments and filings, and reconcile cleared bank transactions.
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