Payroll errors are more than just frustrating—they can disrupt employee trust, delay tax filings, and affect your financial records. Thankfully, if you're using QuickBooks® Online Payroll , most issues can be resolved with a structured, step-by-step approach. Whether it's a miscalculation, missing payment, or incorrect tax entry, this guide will help you find and fix common payroll problems efficiently.
Step 1: Identify the Specific Error
Before jumping to solutions, take a moment to define the problem. Ask:
Was the paycheck amount wrong?
Were taxes calculated incorrectly?
Did an employee not receive their payment?
Was the pay schedule missed or duplicated?
Pinpointing what went wrong helps you apply the right fix—and avoid repeating the same mistake.
Step 2: Review the Payroll Run in QuickBooks
Go to:
Payroll Employees Paycheck List
Here, you can review each payroll processed. Click on the employee's name or paycheck to open the details. Look for:
Incorrect hours or salary amounts
Missing or incorrect deductions
Mismatched tax withholdings
Manual overrides that may have altered the system's calculations
Step 3: Check Employee Setup and Pay Types
Sometimes errors are rooted in how employees are configured. Go to:
Payroll Employees Edit Employee
Verify:
Pay rate, pay type (hourly/salary), and job title
Tax setup (federal and state withholdings)
Benefits and deduction settings
Overtime rules and exemptions
If an employee has been misclassified (e.g., contractor vs. employee), correct it before the next run.
Step 4: Recalculate or Delete and Re-Run Payroll (If Necessary)
If a mistake is found after payroll has been submitted but before it’s finalized, you may be able to cancel and re-run it. Depending on the timing:
For direct deposit errors: Act quickly. Once processed, you may need to issue corrections via adjustments or voids.
For paper checks: Void and reissue corrected checks.
For incorrect taxes: Use Payroll Tax Adjustment tools or contact support for guidance.
Note: Always back up your data or take screenshots before making edits.
Step 5: Verify Your Payroll Settings
Go to:
Gear Icon Payroll Settings
Check:
Default pay schedule
Bank account settings for direct deposit
Tax payment method (auto or manual)
Pay types enabled for your team
Sometimes, outdated or incomplete settings can lead to errors over time.
Step 6: Run Payroll Reports for Clarity
Use these built-in reports to diagnose discrepancies:
Payroll Summary Report
Tax Liability Report
Paycheck History
Employee Details Report
Comparing current and previous pay periods can reveal when and where the error started.
Step 7: Fix Tax Form Errors or Missed Filings
If tax forms were filed incorrectly, QuickBooks lets you amend certain forms. Go to:
Taxes Payroll Tax Filings
Select the form, click View or Amend, and follow the prompts. For complex errors, contact a payroll specialist for step-by-step help.
Step 8: Reach Out to QuickBooks Payroll Support
If you're stuck, don't hesitate to get help. With 24/7 QuickBooks Payroll Support, you can get live assistance from trained professionals who can:
Walk you through corrections
Help file amended returns
Explain system alerts and error codes
Guide you on how to avoid issues moving forward
? Click here for QuickBooks Payroll Support
Conclusion
Payroll issues can feel overwhelming, but they’re rarely unfixable—especially with the right tools. By using this step-by-step approach, you can catch mistakes early, make accurate corrections, and ensure future payroll runs go smoothly. QuickBooks® Online Payroll is built to help you stay accurate, compliant, and confident with every paycheck.
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