The New Shopify + Quickbooks Integration

New Member
1 0 0

Hello everyone. I currently used Zapstich to integrate my Shopify platform with Quickbooks online. It currently syncs the following:

  • Orders and customer data
  • Line items
  • Inventory for COGS
  • Transaction fees
  • Refunds

With this, my reconciliation matching is done in a breeze and I get up-do-date profit/loss information every day.

However, Shopify and Quickbooks just launched their new collaborative integration: or

Has anybody tried it? What are the limitations? Is it limited in features? How does it compare to Zapstitch?

Thank you all.


55 0 47

I am currently a Zapstitch user. I have not tried the Shopify-supported connector yet, but based on teh documentation the key differences I can see are that Zapstitch automatically accounts for Paypal and Shopify Payments transaction fees, making bank reconciliation a lot easier.  Plus it handles refunds - including partial refunds - as well as orders.

That said, Zapstitch seems to have got quite pricey, while the Shopify app is free.  May well be worth a bit of extra work!  Also, based on my own experience, Zapstitch still has a few issues to iron out...

Hope that helps



New Member
5 0 0

I am delighted to see that Shopify is developing a Shopify->QuickBooks Online syncing app. I to would also like feedback on the Shopify app from anyone using it.

We have been using QuickBooks Online (QBO) for over 2 years and Shopify for over a year.  Transmitting and syncing our Shopify data with QuickBooks Online has been easy for us.  A year ago we tried syncing with Zapstitch, but encountered some accounting errors.  (I understand these issues may have been corrected, but we have not tested it.  I am not aware of a way to safely do so, i.e. sync several orders and the undo the sync if there are problems.)

We currently use the eCC Cloud app to sync Shopify Orders, Customers, Products, and Taxes with QBO.  We also use “Shopify Payments” as our payments gateway.  Because “Shopify Payments” deducts their fees prior to issuing a Payout, and since these “Shopify Payments” payouts are batched, it is difficult to match orders/sales receipts downloaded from our bank into QBO with each batched payout.  eCC Cloud in early August introduced a new payment processor that adds a line to each sales order that deducts the “Shopify Payments” fee, so the amount of the batch will match the amount of the payout.  However, it is still difficult to match the individual sales orders with the payout batch.

Unfortunately, I understand the new Shopify Intuit QuickBooks Online app will not eliminate this problem of matching Shopify Payments payouts with batched payouts to our bank account. However, I understand an update is being developed which should eliminate the problem.

eCC Cloud has have recently released an upgrade that modifies Shopify orders, which use the “Shopify Payments” gateway by adding a line to each Sales Receipt that deducts the Shopify Payments fee.  (See attached screen shot of a sales receipt - line 2).

The Shopify Payments are added to an expense account and the transaction is relieved from the Undeposited Funds account and posted to our bank account when we match the downloaded transaction.  

The Sales Receipt number needs to be added to the Reference no. field of the Sales Receipt in order to make the matching of transactions in the various batched payout easier.  Both Shopify and Webgility (eCC Cloud) are aware of this problem and will,  hopefully, soon have a fix.

Shopify Partner
175 0 35

Good question Mike. Thanks for your kind words on your experience with Pipemonk (formerly ZapStitch). 

Hi all, 
While we wait for our awesome community to share their review of Shopify's app, here are some key differences in approach and features that we have identified:

We are closely listening to our customers and are inspired by their reviews. Here's a detailed post on the comparison. Would love to hear your questions. 

55 0 47

I have been using Zapstitch (now Pipemonk) for nine months now, integrating Shopify (including Shopify POS transactions) with QBO, and using both Shopify Payments and Paypal gateways.  In terms of features it would be difficult to beat. As well as syncing orders,it handles refunds (partial and full) and also deducts Paypal/Shopify Payment fees into a separate expense account, simplifying reconciliations dramatically. It also syncs inventory and products. It doesn't automate the process of grouping payments via Shopify Payments into payouts, but as the payments go into an undeposited funds account, the task becomes relatively simple in QBO using the Shopify Payments payout reports in Shopify.

There are multiple options on initial set-up, including whether you want customers synced across or all orders grouped under a single QBO customer, whether you want inventory synced and if so which way, etc. etc. , so loads of flexibility.

I have had a couple of accounting-related problems since starting - all related to my being UK-based and the software having been written mainly with the US in mind, and in particular without a full understanding of UK VAT rules.  However, once reported the issues were dealt with quickly and have been fixed.  I have also had a couple of technical issues very recently, which appear to be linked to their introduction of a major new software release, but again support has been very responsive and the issues have been dealt with effectively and quickly.

Overall, I am happy with my choice and would recommend it to others.  I haven't looked at the new free Shopify app in any detail as it doesn't support non-US users, but based on what I have read it would appear to be a pretty basic order-sync app, with nothing like the functionality of Zapstitch/Pipemonk.   I HAVE looked at other paid-for connectors like One-SAAS, ECC, Cloud Connector, and as far as I can see Zapstitch beats them significantly on functionality.

Advice for anyone looking at connectors like this - think about:

1. Are you happy to have to handle refunds manually?

2. How easily can you reconcile payments to bank transactions in QBO when the payment amounts don't tie in with the bank transactions?

3. Are you going to hold  inventory in QBO (requiring QBO Plus)?  If not, how will you do you calculate COGS as part of producing your P&L?  If so, you'll want to be able to sync inventory changes (reciepts from suppliers, stocktake amendments, etc.) up to Shopify from QBO.  

There's a lot more to it than just feeding orders across....

Dan Bernard 



New Member
1 0 0

I thought there isn't an area within Shopify to enter COGS by item.  So if there isn't, how is COGS then calculated within QBO?  I understand if an order sync's over to QBO the Sale will be recorded, but how is an associated cost recorded without there being a COGS for that item entered?

Does this require sycning your product list from Shopify to QBO, and then somehow manually uploading a COGS figure into the line items in QBO after the fact?

6 0 2

There needs to be more ways to integrate a Shopify website w/ Quickbooks POS/ Point of Sale.                      I have 2 brick and mortar stores, and a shopify website and need my inventory to sync between the them all. 

55 0 47

What do you use as a till system for yoyr brick & mortar stores?

Not applicable
1629 0 0


I am currently using the Shpoify QBO Quickbooks Online needs a tremendous amount of improvement as well as a helpful user guide on how and when to use it. For example, when exporting paid orders from your Shopify store to QBO, the export is incomplete. The billing and shipping address are missing the Company & Contact Name on the order. If there is something I am doing wrong, I would appreciate the help, otherwise stay away from this app it leaves you disappointed just like a few other Shopify apps' inadequacies. e.g. packing slip and invoice printing. OMG!