I can see how frustrating if there's a duplicate transaction on your book. I'll explain to you the possible causes of why this is happening in QuickBooks Online Account.

An error might occur if the bank transaction isn't to your payroll or employees' paychecks. I suggest un match your bank transaction and re-match it. 

Here's how:

1. Go to Bookkeeping. Select Bank transactions or go to Banking.
2. Select the tile for the bank or credit card account you downloaded the transaction.
3. Select the Categorized tab.
4. Find the transaction you want to unmatch.
5. Select the blue transaction link in the Added or Matched column to see the matched transaction.
6. Select Undo from the Action column.

Once you undo it, This resets the transaction QuickBooks tried to create for you. Go back to the For Review tab and categorize the transaction.

Then, match the downloaded transaction with the one you already entered. It connects the transaction so that there aren't any duplicates.

1. Find a downloaded transaction with the Match option in the Action column.
2. Note the Date, Description, Payee, and amount spent or received.
3. Select the downloaded transaction to expand the view.
4. Review the Matching records found in QuickBooks. It is the possible matching transaction you already entered in QuickBooks.
5. Select the link next to each match to get more details.
6. Make sure this is the correct match. In particular, review the Deposit to, Payment method, and Bank account fields on forms for the existing transaction in QuickBooks.
7. If this is the correct match, close the open transaction.
8. Select Match.

I'm also adding this article for your guide on how to fix the issue on your reconciliation: Fix issues at the end of a reconciliation in QuickBooks Online.

Know that I am always here to support you. Please let m know if you have other concerns. Keep safe.

Anyone can figure it out about this situation yet?  I also have the same issue and I still don't know what to do.  I voided the payroll check (DD) because I think it booked twice but maybe it incorrect.  Now I don't know what I do for correct it.  Please advise.  Thanks.

Hi,

I am in Australia so not sure if it is relevant for you, but this is how I handle my payroll bank transaction.

When I do a pay run, QBO automatically does the journal entries for this transaction.  It debits the Wage Expenses account and credits the Payroll Clearing account.

Therefore when I am in the bank feed, I put the wages amount I paid as a transfer to the Payroll clearing account.  This should balance out the Payroll clearing account.

You can check what account your version uses by going to Chart of Accounts.

Hope that helps.

Hello,

I finally figured this out today and I just wanted to share.

You go to the gear icon then payroll settings

click on the pencil by accounting at the very bottom

then go to update transactions. 

I just updated all my transactions for the year and some how that fixed it. It almost seemed to easy to be true. I hope it works for yours, as well. 

Hi! I will start saying I am no expert, just a user with the same or a very similar problem, so please be cautious if you decide to listen to me.

In my case, my payroll account was increased in random days only, counting two times the salary of one or two employees, not all of them.

I followed the first answer in here about undoing the match and matching it again, and did not work, but I noticed that only the “duplicates” had an option to match with a “payroll expense”, and not only with paychecks like the others.

So I went to my checking bank account (in quickbooks, (from my balance sheet), and I found extra lines with the duplicate amounts. I compared with my bank statement, to confirm, and yes, they were extra lines that I never input.

So, I changed those lines values to $0 (I guess you can delete them completely if you want), and I got what I was expecting in both, my P&L and my bank account (balance sheet).

I am not expecting any issues in the future after the changes, but will post if I find/observe any problems.

Hope this helps. Have a nice day!

Ran into the same problem. Quickbooks would record the gross amount for each employee on pyroll, as well as the net amount. Resulting in my numbers being astronomically high, and wrong. 

I never used the "Match" feature while categorizing. (Mainly because i didn't quite know what it does tbh). After reading these messages, i decided to do some expirementing. I went back and undid every payroll transaction, and then Matched them. With full trust in the system, it worked. I now have all the gross amounts under "payroll wages", and the taxes under "payroll taxes" 

I hope this helps.