Fix Payroll Calculated Twice In Accounting Software | 2026 Help

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:

Go to your chart of accounts

Locate payroll expense accounts

Find and delete manually created payroll journal entries

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.