Showing results for 
Search instead for 
Did you mean: 
Level 1

PayPal for Nonprofit

I have never dealt with Paypal until given this assignment for a nonprofit in quickbooks online. I understand donations come in and a transfer is done that appears to show in the bank feeds to the checking. Then it shows in the Paypal bank  and then in the paypal clearing with a negative amount. How do I handle this and then do the Paypal Bank and Paypal Clearing accounts both get reconciled and which first. Currently the Paypal clearing is a negative amount. So confusing. Paytraqer is used on this, but not sure of it's purpose. I would sure appreciate any help. Thank you.

2 Comments 2
QuickBooks Team

PayPal for Nonprofit

Hi there, @Ponz1. I'll be sharing with you some information about handling PayPal transactions in QuickBooks Online (QBO).


Once you connect PayPal to QuickBooks, you can edit, categorize, and match PayPal entries the same way with other bank transactions. In this case, you can reconcile your PayPal bank entries the same as with the regular bank accounts. 


Here's how:


  1. Sign in to your QBO account.
  2. Go to the Gear icon, then click on Chart of Accounts.
  3. If you're reconciling for the very first time, select Get started to continue.
  4. From the Account dropdown, select your PayPal bank. Make sure it's the same one on your statement.
  5. Review the Beginning balance. Make sure the beginning balance in QuickBooks matches the one on your statement. Here's what to do if they don't match.
  6. Enter the Ending balance and Ending date on your statement. Some banks call the ending balance a "new balance" or a "closing balance".
  7. If you see it, review the Last statement ending date. This is the end date of your last reconciliation. Your current bank statement should start the day after.
  8. Click Start reconciling when you're ready.


If the PayPal Clearing account is just used for transferring amounts or as a washing account, then there's no need for you to reconcile the account. If it's necessary to reconcile both accounts, then you can start either way.


For more tips about reconciliation, open this article: Reconcile an account in QuickBooks Online.


In case you want to generate a reconciliation report for future use, you can refer to this link as your guide: How do I view, print, or export a reconciliation report?.


Please feel free to leave a comment below if you have any other follow-up questions with PayPal reconciliations. I'll be right here to help. Keep safe!

Fiat Lux - ASIA
Level 15

PayPal for Nonprofit


Afaik, PaytraQer is used to automate the flow of data from PayPal to QBO.


When you need to reconcile PayPal transactions, we recommend our clients with another app.


Need to get in touch?

Contact us