Most ecommerce shopping cart software today claims that they will integrate with QuickBooks. What exactly does this mean?

Typically, it means that the ecommerce software will produce a an Intuit Quickbooks.iif file or in some cases simply an orders.csv file which must then be imported into QuickBooks Accounting. You can export your orders from your website and then import them into QuickBooks accounting as often as required, be it once a day or once a month.

What these ecommerce shopping cart softwares don’t tell you is that there are two different QuickBooks software programs: Accounting and Point of Sale. When an ecommerce shopping cart program claims integration with QuickBooks, it is almost always talking about the Accounting program and not the Point of Sale Program. Often, that is not what the small business owner is looking for. Sure, it great to be able to reconcile your accounting, but the small business owner who has both a physical store and an online store is also concerned with inventory. If a product is sold online, they want there in-store POS system to recognize that an item has been sold and is removed from the inventory.

Online only stores don’t have this problem – they only have a single source of inventory. And very large companies like Walmart don’t pull inventory out of a store to fulfill an online order – they are two different sets of inventory. But for small companies, this becomes a very real problem and ecommerce shopping carts don’t address this. A large part of the reason of course is security – if your online store is connected to the same database as your brick and mortar store, you can have a very real security breach. As a result, shopping carts address integration only with the Accounting program from QuickBooks.


There are actually 3 levels of integration that you may want to consider: QuickBooks Accounting, QuickBooks Payments, and QuickBooks Point of Sale.

QuickBooks Accounting

As I said, this is what most shopping cart software considers when claiming integration with QuickBooks – being able to export a file that you can them import into your QB Accounting program in order to account for your income from your online store. Most shopping cart software can do this.

QuickBooks Payments

Every shopping cart software supports different payment methods. The most common of course is PayPal, followed by various payment processors such as Authorize.net. If you are looking for a shopping cart that can accept Intuit Merchant Services, your choices are limited. Many carts, including ECwid do not support Intuit Merchanct Services as a payment method, so if this is important to you, do your homework. Shopp, WooCommerce, Shopify, and BigCommerce all have add-on modules that provides credit card processing from Intuit that can sync transactions to QuickBooks. The Intuit Merchant Service add-ons provide secure credit card processing directly on your website so shoppers checkout and you get paid with your Intuit Merchant account. This does not affect inventory – just the payment method. And each shopping cart provides different levels of a seamless experience for both the customer and the shop owner.

QuickBooks Point of Sale

Integrating in real-time with QuickBooks Point of Sale requires some clarification, as the POS program from QuickBooks comes in several versions, including Basic, Pro, and Multi-Store. A Multi-Store POS requires that inventory is synchronized across both the website and the inventory in each store. In order to do this, the database must reside on the cloud and not on your local computer. There is a software from IAmodules (http://www.iamodules.com/WSW/QuickBooks-Point-Of-Sale-ECommerce.jsp) that does this.

Other POS options

The alternative is to use a POS system that is designed to work with your ecommerce shopping cart – essentially turning your online store into a POS system for your brick and mortar store. That way, the data is also stored in the cloud behind a secure firewall, and you can sync your inventory. For example, there is a plugin that works with WooCommerce called WooCommerce POS that does this.

On September 16, 2015 (yes just this week), WooCommerce announced that it was providing integration with the LightSpeed POS system. This is huge, as long as someone is using LightSpeed – unfortunately, many small brick and mortar business use QuickBooks POS, not LightSpeed.

So back to the question, what ecommerce shopping carts integrate with QuickBooks? If all you are looking for is to integrate with QuickBooks Accounting, most of them will work including WooCommerce, ECwid, Shopp, BigCommerce, and Shopify using the export/import feature. Some carts, including WooCommerce and Shopify offer their own POS systems. A few carts, including WooCommerce, Shopify and BigCommerce, offer additional modules or “apps” that can be purchased to also integrate with QuickBooks POS, but since this means that the data must now reside on the cloud and not on your local computer, there is a charge. Often, these modules or apps are written and maintained by a third-party. For WooCommerce, the app is available from 61extensions and costs between $129 and $249. BigCommerce uses 3rd party apps by T-Hub and Webgility eCC (eCommerce Connector). In the case of Shopify, the app is called “Shoplink Integrator” and costs $39.99 to $199.99 per month. This is in addition to the monthly charges and transaction fees already charged by Shopify.


Webgility eCC Desktop is a PC application that is downloaded and installed onto your computer. eCC Cloud works with leading platforms, including Amazon, eBay, Etsy, WooCommerce, Magento and Volusion.  The cost for eCC ranges from $1,500 to $3,900 per year. If you are interested in integrating your web store with QuickBooks, eCC is the best way to handle this, regardless of the store platform you use. You can get more information here: http://mbsy.co/webgility/90310