QuickBooks Payroll Essentials

Updated 10/20/2026.

End-to-end payroll for bookkeepers: choose the right QuickBooks payroll product, set up companies and employees, run payroll, manage tax payments and filings, produce forms, handle workers' comp and compliance, close the year, and troubleshoot common problems. Taught on current QuickBooks Online and Desktop payroll products.

Who it is for: Bookkeepers responsible for running payroll and payroll tax compliance for QuickBooks clients.

Length: about 120 minutes, 8 modules, 50 quiz questions, certificate of completion.

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What you will learn

Choose the right QuickBooks payroll product for a client by comparing current QuickBooks Workforce tiers and Desktop payroll options, and explain what Intuit files and pays on the client’s behalf.
Set up payroll in QuickBooks Online and Desktop, including company settings, employee records, pay types, deductions, contributions, and contractor 1099 tracking.
Run a payroll cycle, review pay details, handle direct deposit lead times, print paychecks and pay stubs, and process off-cycle or bonus payments.
Manage payroll tax payments and filings, including e-file and e-pay enrollment, payment schedules, and liability tracking in QuickBooks.
Produce and file federal payroll forms (941, 944, 940, W-2, W-3, 1099-NEC) from within QuickBooks Online and Desktop.
Set up workers’ compensation tracking, manage garnishments, report new hires, and maintain payroll records in compliance with federal and state rules.
Execute a year-end payroll checklist, including W-2 and 1099 review, final tax payments, and January start-up tasks.
Troubleshoot common payroll problems, including liability balance discrepancies, incorrect paychecks, misrecorded liability payments, and prior-quarter adjustments.

Course outline

Module	What it covers
Choosing a QuickBooks Payroll Product	Compare current QuickBooks Workforce tiers, Desktop options, and cost drivers
Setting Up Payroll: Company, Employees, and Payroll Items	Complete the setup interview, employee records, pay types, and contractor tracking
Running Payroll: Paychecks, Direct Deposit, and Taxes	Create payroll runs, handle direct deposit, print checks, and manage off-cycle payments
Payroll Tax Payments and Filings	Manage tax liabilities, schedules, and electronic filing
Payroll Forms: 941, 940, W-2, and 1099-NEC	Produce, review, and file the federal forms your clients need
Workers' Compensation and Payroll Compliance	Track workers' comp, handle garnishments, report new hires, and keep solid records
Payroll Year-End Checklist	Close the year cleanly and start January with confidence
Troubleshooting Payroll Problems	Fix liability discrepancies, misrecorded payments, and prior-quarter errors

How the course works

Each course is self-paced. Slides unlock as you read them, most carry a short check, and every module ends with a quiz you pass at 80 percent. A final assessment and a signed attestation complete the course, and you receive a certificate of completion.