Why am I missing payroll transactions even thou it QuickBooks shows them as processed?

Paychecks can be missing when the bank from your accounting preference isn't the same as the bank's where you download wage expenses, @HeadsHurtin. Since this is a processed direct deposit, you can correct this by creating a Journal Entry (JE) to transfer the amounts to the correct bank account. Let me share the route to resolve this as soon as possible.

Just a heads up, make sure to consult your accountant before doing this to keep your records accurate and be able to match the bank transaction with the correct JE transaction. But first, you'll have to verify if the paycheck transaction in QuickBooks has the correct bank account. Here's how:

1. From your Paycheque list, select the paycheque you want to verify. (Optional) You can click Filter▼ to change the Date range or Employee.
2. Click the paycheque that you want to verify.
3. See if it has the correct bank by viewing the Paid from label. You can also click the Transaction Journal to see account postings.
    
   
   

If it is correct and the system is just not finding a match, you'll have to match those paychecks manually. Then, by clicking the downloaded payroll transaction, you'll see the Match radio button and be able to match it accordingly from the Find other matches window. Take note that you'll have to utilize the Filters icon to narrow down your searches by allowing you to enter a starting and ending date as well as picking Cheques as the Record type and be able to check the paycheck boxes. See this guide for more insights: Match online bank transactions in QuickBooks Online.

Otherwise, please proceed to create a JE to post the amounts on the correct bank account and date (this will be recognized as the paycheck date when matching it to a payroll bank transaction). If you don't have an accountant, I suggest visiting this site to find a certified QuickBooks ProAdvisor to help you debit and credit the accounts: Find an accountant. Alternatively, refer to this article to learn how to debit and credit a paycheck transaction: Record payroll transactions manually in QuickBooks Online.

Once all is well, continue to match this JE to your downloaded bank payroll transaction by following the instructions I've implied above. Additionally, ensure editing your payroll accounting preferences by changing the bank account so your paycheques post to the appropriate account moving forward, let me show you how:

1. Click the Gear icon and then select Payroll settings.
2. Scroll down and then click the Pencil icon on the Accounting section.
3. From the Bank account label under Paycheck and payroll tax payments, click the Pencil icon.
4. Pick the correct asset from the Bank Account drop-down.
5. Hit Save.
   
   
    

And you're on another level of getting all things back on track. I'd like you to review this article as part of the guide that I've presented: View the Transaction Journal for paycheques in QuickBooks Online.

On the other hand, you've mentioned that you were able to look at the wage expense. Are you referring to the Expense|Wage quick report? From this statement, you can adjust the Report period to either, All Dates or a Custom date to narrow your tracking paycheques.

Furthermore, by making sure every payroll record is aligned and just right, feel free to view a list from this article for other payroll reports that you can run: Run payroll reports. Also, this might as well come soon as a feature with your current subscription: Automatically match QuickBooks online product transactions.

This detailed information can be quite challenging to search for payroll records to match them with your bank transactions, but please always get back here if you need more assistance viewing missing payroll transactions made in QuickBooks or any product issues that might disrupt your business workflows. Anytime I will come to lend a hand. Stay safe and well, @HeadsHurtin.