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megan53
November 25, 2021
Solved

Shopify / Paypal / eBay / Stripe - How would you navigate Quickbooks for this setup

  • November 25, 2021
  • 3 replies
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We have Quickbooks setup to automatically sync transactions from our bank account.

 

However this does not:

* track sales

* track receipts

* track fees per sale

 

We've tried the Shopify Quickbooks integration, but the act of syncing sales duplicates our turnover. The reason being, automatch doesn't work due to the 1-2 day delay in receiving the payment, plus the price mismatch due to the fees taken by shopify.

 

We've tried using the Paypal integration, however this again duplicates the turnover rather than matches it.

 

As far as we can see, the only way to get an accurate picture of our accounts, is to manually enter the sales and the fees. Is that correct?

Best answer by GebelAlainaM

I'm happy to see you here in the Community, @megan53. I'll make sure that this issue gets sorted out today. 
 

I also agree with you. You'll need to manually record the sales and fees to avoid duplicate transactions from Paypal. To do that, you can follow the steps below:

  1. Scroll down to the Add funds to this deposit section.
  2. Enter the fee as a line item.
  3. Select who the fee was from (ex: the bank charging you).
  4. Select Bank Charges from the Account ▼ dropdown.
  5. Enter the amount fee as a negative number. For example, if the fee was GBP £ 50, enter –50.
  6. Review the deposit total with the bank fee.
  7. Select Save and close or Save and new.

Right after, ensure that the amount matches your bank's net income.

For further understanding on how to record and make bank deposits in QuickBooks Online, you can visit this article.
 

You'll also need to contact the third party app support to review the setup. Here's how to contact the Developer Support:

  1. Go to Apps.intuit.com.
  2. Type in the Paypal app in the search bar.
  3. Select the Contact tab or the Support tab.

Please keep me posted in comment section if you need further assistance. I will be happy to guide you. Have a wonderful weekend!

3 replies

G
GebelAlainaMAnswer
November 25, 2021

I'm happy to see you here in the Community, @megan53. I'll make sure that this issue gets sorted out today. 
 

I also agree with you. You'll need to manually record the sales and fees to avoid duplicate transactions from Paypal. To do that, you can follow the steps below:

  1. Scroll down to the Add funds to this deposit section.
  2. Enter the fee as a line item.
  3. Select who the fee was from (ex: the bank charging you).
  4. Select Bank Charges from the Account ▼ dropdown.
  5. Enter the amount fee as a negative number. For example, if the fee was GBP £ 50, enter –50.
  6. Review the deposit total with the bank fee.
  7. Select Save and close or Save and new.

Right after, ensure that the amount matches your bank's net income.

For further understanding on how to record and make bank deposits in QuickBooks Online, you can visit this article.
 

You'll also need to contact the third party app support to review the setup. Here's how to contact the Developer Support:

  1. Go to Apps.intuit.com.
  2. Type in the Paypal app in the search bar.
  3. Select the Contact tab or the Support tab.

Please keep me posted in comment section if you need further assistance. I will be happy to guide you. Have a wonderful weekend!

Fiat Lux - ASIA
Fiat Lux - ASIA
November 26, 2021

@megan53 

Explore these apps to reconcile your transactions and avoid any duplications

https://synder.grsm.io/quickbooks

https://www.a2xaccounting.com/ ---> use promo code FL_10_6MON_2021

 

S
Samantha Blake
May 22, 2025

We had the exact same setup — Shopify, PayPal, Stripe, and eBay — and ran into all the same issues with QuickBooks. Syncing from our bank looked fine at first, but:

  • It didn’t track sales, fees, or receipts properly

  • Shopify & PayPal syncs just duplicated revenue

  • Matching was impossible because of delays and fee differences

We tried a few options, but Synder was the only thing that actually worked.

It connects all those platforms (Shopify, PayPal, Stripe, eBay) and syncs each transaction correctly:

  • Sales, payment processor fees, and even refunds are tracked accurately

  • No duplicate income

  • Everything matches automatically, so we don’t need to manually adjust or enter anything

It seriously cleaned up our QBO reports and saved hours every week. Once it’s set up, it just runs in the background.

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