How to Stop Payroll from Counting Twice in Your Account (2026 Guide) 

Payroll errors can be frustrating—especially when your system counts payroll twice, inflating expenses, throwing off reports, and creating tax confusion. This issue is common in accounting and payroll software and usually happens due to sync problems, duplicate entries, or incorrect setup.

In this guide, you’ll learn how to fix payroll double counting, prevent it from happening again, and ensure your books stay accurate. If you need immediate assistance, call +1-866-409-5111 for expert payroll support.

Why Is My Payroll Being Counted Twice?

Before fixing the issue, it’s important to understand why it happens. Payroll duplication usually occurs due to one or more of the following reasons:

• Manual payroll entries added on top of automated payroll
  
  

• Payroll service synced more than once
  
  

• Incorrect payroll account mapping
  
  

• Payroll journal entries not excluded from reports
  
  

• Software migration or upgrade errors
  
  

These issues cause double payroll expenses, incorrect liabilities, and misleading profit & loss statements.

How to Fix Payroll Being Counted Twice (Step-by-Step)

1. Identify Duplicate Payroll Transactions

Start by reviewing your payroll expense reports and general ledger.

• Look for identical payroll amounts posted on the same date
  
  

• Compare manual journal entries vs. payroll-generated entries
  
  

• Check if payroll was imported more than once
  
  

This is the most common cause of duplicate payroll entries.

2. Remove Manual Payroll Journal Entries

If you’re using automated payroll services, manual entries are not needed.

Steps:

1. Go to your chart of accounts
   
   

2. Locate payroll expense accounts
   
   

3. Find and delete manually created payroll journal entries
   
   

4. Save changes and refresh reports
   
   

Removing these entries usually resolves payroll double counting issues instantly.

3. Check Payroll Integration & Sync Settings

Sometimes payroll syncs twice due to connection errors.

Verify the following:

• Payroll service is connected only once
  
  

• Sync history does not show duplicate imports
  
  

• Payroll clearing account is mapped correctly
  
  

Improper syncing is a major reason payroll shows twice in reports.

4. Review Payroll Clearing Accounts

Payroll clearing accounts act as a temporary holding account.

If not configured properly:

• Expenses may post once from payroll
  
  

• Then post again when bank transactions clear
  
  

Ensure payroll clearing accounts zero out after each payroll run to avoid payroll expense duplication.

5. Run Corrected Reports

After fixing entries:

• Re-run Profit & Loss
  
  

• Check Balance Sheet
  
  

• Compare payroll totals with payroll summary
  
  

This confirms your payroll is no longer being counted twice.

How to Prevent Payroll from Being Counted Twice Again

Follow these best practices to avoid future issues:

• Use one payroll method only (manual OR automated)
  
  

• Avoid editing payroll journal entries
  
  

• Reconcile payroll accounts monthly
  
  

• Audit payroll reports regularly
  
  

• Document payroll setup changes
  
  

Consistency is key to preventing duplicate payroll accounting problems.

FAQs

Why does my payroll show twice on my profit and loss?

Because both automated payroll and manual journal entries are recording the same payroll expenses.

Is it safe to delete duplicate payroll entries?

Yes—as long as they are manual duplicates and not payroll-generated transactions.

Can payroll duplication affect my taxes?

Absolutely. Double-counted payroll can lead to incorrect tax filings and overreported expenses.

How do I know which payroll entry is correct?

The payroll-generated entry from your payroll service is typically the correct one.

Who can fix payroll counted twice quickly?

Call +1-866-409-5111 for fast, expert payroll troubleshooting.