Here’s a Better Way to Integrate Shopify with Quickbooks

Here’s a Better Way to Integrate Shopify with Quickbooks


There are times when the Shopify app for Quickbooks is useful, but in many cases, it’s more detail than most business owners need. And with the additional fee for automatic integration, figuring out a time-saving (and free) solution is important to help control administrative costs and eliminate human error.

In this video, you’ll learn my alternative method for entering Shopify Sales into Quickbooks. This way isn’t automatic, but it’s an easy way to track your Shopify transactions in Quickbooks with all of the useless data filtered out.

(This video is shown with Quickbooks Online, but the process would be similar with Quickbooks Desktop).

To get a full rundown of the pros and cons of using the Shopify app for Quickbooks, read the full blog post here:

For more bookkeeping tips on my channel, you can watch the entire bookkeeping playlist here:

Michelle Mangen is the founder of Your Virtual Assistant, a business that provides comprehensive virtual bookkeeping services.

Michelle formerly worked in upper management with a property developer and property management company in Milwaukee, WI. Michelle and her staff had to learn how to keep things running smoothly without always having the resources to keep up. From this experience, Michelle learned how to increase productivity by using automation and other efficiency-enhancers to help get more done in less time.

Your Virtual Assistant was born out of a desire to help sole proprietors and small businesses reclaim lost time spent on their accounting and bookkeeping tasks. By helping to offload these tedious (but important) business tasks, Michelle supports business owners while they balance their work/life schedule. With the unique blend of productivity and bookkeeping/accounting expertise, Michelle takes on time-consuming business tasks and completes them faster while preserving meticulous details.

Please rate and comment on this video if you have any questions or you’d like to see more videos like this!

If you need virtual bookkeeping services, click here:

If you’d like to find a comprehensive virtual bookkeeping package, click here:

If you know you need accounting and bookkeeping services but don’t know where to start, feel free to contact us and we’ll discuss options related to your business:

Want to learn how to make an easy online address book? Click here:

Process QuickBooks transactions faster with these simple naming tweaks:

Learn how to easily create mailing labels in Excel and Word:

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  1. Is the Returns/Refunds you've added to the sales receipt an income account that will have a negative balance or is it a different type of account? Also, on the refund receipt, would you want to add the adjusted shopify fee refunded back or leave it off the refund receipt?

  2. With this method, how (if at all) do you account for your Cost of Goods Sold? And do you have a way that you can break out your refunds, fees, adjustments, discounts from your income? Very interested in how it all works together with the other Seller Channels you have hooked in there. Do you create a non-inventory product for each line item on each sales receipt? So do you keep all your real inventory and customer data in their respective platforms (ie Amazon, Shopify, etc.)

  3. It's very useful!!! but Total Sales on the Sales Tax Liability Report is different from the Profit and Loss Report Total Income. In my case, at the Sales Tax Liability Report, the total sales of the sales tax report are the total sales less the merchant fees. was the error came from the product/merchant fee setup? any suggestion would help. Thanks,

  4. Thank you for sharing this! Can you please elaborate on how you set up your Merchant Fees and Refunds line items for recording Shopify Payout transactions? I just created a new Merchant Fees item in my Item List in QB Desktop. When prompted for the item "Type", I chose "Other Charge" and I linked it to my existing "Shopify fees" Expense Account. Is that appropriate for this application?

  5. I have a credit a deduction from shopify due to a return. When entering a sales receipt, QB will not allow me to enter a negative amount. How do I account for this when shopify took money out of my account due to a return for a particular day?

  6. Solid manual method for very small Shopify sellers.

  7. I'm trying to learn how I would enter COGS for a net payout. We sell earrings and all of our products cost the same. So, I love the idea of using your suggested method to avoid Quickbooks Plus and the monthly cost of the integration tool.

    How would I enter the COGS and tie it to the Shopify payout?

  8. Great video, terrible title, it took me like 3 minutes to even figure out what the video is about

  9. Hi, just a quick question. Since shopify sends payouts after 2 days, do we record transactions on the date that we made a sale or on the payout date?

    Just started shopify aliexpress dropshipping a few weeks ago and now getting sales and using an excel spreadsheet for now and wanted to know what the common practice is with bookkeeping via dropshipping, shopify…

  10. what version of quickbooks online do you use?

  11. Michell – if one wanted to keep things super simple and just track income vs expenses. Couldn't you just keep the payouts in quickbooks as net payouts (or withdrawls in the case of a refund that exceeds the days sales)? We used to track inventory and cost of goods and such but I'm looking to simplify our very small business and just record income/expenses. So, in our case I'm thinking we'd just record shopify net credits/debits and write checks to vendors and keep it at that. Am I missing something?

  12. Hi, so you have to manually do this for every day you get payed out? Is there no way to automate this?

  13. I have a question about using Paypal in Shopify as well. Is there an easy way to separate the different payments. I am not finding totals from the two, easily reported. This may not be the proper way to ask this. Trying not to have double entries through shopify and Paypal.

  14. Is there any update to where all you do is connect Shopify, Paypal and QB and it just automatically does everything?

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