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How-To Guide: Seamlessly Integrate Shopify with QuickBooks
Aug 15, 2019

How-To Guide: Seamlessly Integrate Shopify with QuickBooks

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Estimated reading time: 12 minutes.

Shopify A2X

Automating the accounting side of your ecommerce business is a smart step.

Not only are you ensuring accuracy and consistency over the lifeblood of your business, but you are gifting yourself the time to invest your resources elsewhere.

When you integrate Shopify with QuickBooks, your store transactions are uploaded and stored automatically. When you add A2X into the mix, the details within these transactions are captured and displayed for you, ensuring that you have all the information you need, as an ecommerce seller, about your financial activity.

There are a host of benefits to using these three platforms in sync. By the end of this article, you will know not just how to integrate Shopify with QuickBooks, but how to get the most out of your app integrations and where to get the most up-to-date information to support you in your journey.

In this guide:

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Shopify Apps to Automate Your Business

There are two major advantages to automation:

  • It ensures accuracy and consistency in repetitive tasks.
  • It frees you up to spend your time and energy elsewhere.

These are two pretty big advantages that directly correlate to the success of your business.

If you’re here, you are probably already covered on the accounting software side, which is great: getting your accounts right is crucial to growth.

What about the other areas of your business that can be automated? There are plenty of them:

  • Processing orders
  • Tracking orders
  • Data and email capture
  • Inventory counting and management
  • Marketing
  • SEO
  • Printing labels
  • Social proofs

The best apps to choose will depend on your business needs. Consider which areas take up the most of your time that you would like to spend elsewhere.

Perhaps you have a marketing background, and would rather automate order tracking and processing which don’t need your expertise. Equally, you may know nothing about SEO or social media advertising, so need help with that.

Your tech stack should meet your unique needs and play to your strengths. Even if you don’t wish to use an accountant up front, it may be helpful to consult them in the beginning to decide your best strategy. See our directory here for our trusted partners.

For a breakdown of our favourite apps in the above categories, check out this blog.

Level-Up Your Shopify Integration with QuickBooks with A2X

Whilst a Shopify QuickBooks Online integration is incredibly useful and efficient, there can be some crucial detail missed without the services of A2X.

A2X acts as an interpreter between the two platforms, ensuring that you get every piece of information related to your transactions that you need.

Each deposit into your bank is the end result of a few steps: Shopify fees have been taken, sales tax collected, perhaps shipping costs were included or reimbursements received. Even currency differences might be applicable.

When all of these elements are represented by one final number, you miss a lot of information. Without A2X, these crucial puzzle pieces for your balance sheet are lost.

Never miss a detail again with A2X for Shopify.

A2X not only imports your Shopify payouts and sales automatically, posting them to QuickBooks in a way that is easy to reconcile, it also catches all the information that you need to be on top of your accounts and your business performance in general.

Shopify A2X

A2X is a must-have for Shopify sellers because it offers:

  • Quick reconciliation: A2X reconciles your Shopify payments perfectly including all fees quickly, saving you time.
  • Reliable numbers, always: A2X automatically imports your Shopify data and accurately, so that you can rely on your numbers to make important decisions about your business - like when to scale, what to spend on marketing, and when to pull back on expenses. You’ll have a more honest picture of your business.
  • The accrual accounting method: Without A2X, QuickBooks will import fully paid orders instead of importing transactions as they occur. A2X uses the accrual accounting method instead, reflecting that income and expenses generated in one month can carry over into the next month or even longer. This will also help give you a bird’s eye view of your business and its performance, with reports that truly reflect your month-to-month cash flow.
  • The ability to grow with you: A2X scales as you grow to support thousands of daily orders without passing on those individual orders to your accounting system (and clogging it up). By sending journal summaries of your orders, rather than the individual orders themselves, A2X keeps your accounting system organized and clear of clutter without losing your important data.
  • Multi-channel support: A2X supports multiple Shopify stores that connect to a single accounting system, if you sell on more than one channel.
  • Multiple payment gateway support: A2X supports multiple payment gateways, as many Shopify sellers use more than one.
  • Multi-currency and tax rate support: A2X supports multi-currency sellers and multiple tax rates for cross-state or country sales.

The good news is, you can test out these benefits for yourself on a free trial!

Sign up here before you get started with your Shopify QuickBooks integration.

Step-by-Step: Integrate Shopify with QuickBooks Online

Here’s our step-by-step guide on Shopify and QuickBooks integration with A2X, with steps, below.

  1. If you haven’t already, sign up for your free trial of A2X for Shopify. You can then log in to A2X via Google or Intuit.
  2. You will need to select “Create an Account” and enter your details.
  3. Once you have entered your details and given permission to Google to log in, you’ll have a dashboard that looks like this:

Next, you’ll need to connect to Shopify.

  1. Under the Shopify logo, click the button “Continue with Shopify”. You will be asked to enter your store name and then click “Connect”.
  2. You will be redirected to your Shopify store and be asked for permission to allow A2X access:

Shopify screenshot

  1. After granting permission, you will be taken back to A2X and your first payouts will automatically begin populating. This could take as little as 10-20 minutes for smaller stores and a few hours for larger.
  2. Once imported, you should see something like the below:

A2X reconciliation

The next step is to connect to QuickBooks.

  1. You should see the option to “Connect to QuickBooks” in the same place that you were able to connect to Shopify.
  2. As with Shopify, you’ll be redirected to your QuickBooks account to grant permission for access by A2X, and then brought back to A2X again when done.
  3. Check the Connections screen to check both your accounts are linked to A2X.

The last step is optional but highly recommended: Accounts and tax mapping.

The Accounts and Taxes feature allows you to map how your Shopify payouts arrive into QuickBooks.

By mapping out your tax categories ahead of time, you can ensure that the data A2X sends to QuickBooks is recorded according to your instructions from the beginning.

Imports will be coded and ready to reconcile automatically.

Taxes in A2X

You will need to create a Chart of Accounts (either from scratch or using some generic suggestions from A2X), which A2X will use as a blueprint.

  • You can set the accounts that the transactions will be coded to in the Accounts and Taxes tab on your A2X dashboard.
  • To choose your Chart of Accounts, access your accounts in QuickBooks by clicking the ‘x’ next to each account in A2X, and selecting from the drop-down menu (see below).
  • Click the “Save Mapping” button at the bottom of the page when you’re done or make any changes.

Tax mapping

Note: If you create new accounts in your QuickBooks after connecting A2X, you will need to clear your cache in Settings and Connections.

For more help and instructions on this step, check out our tutorial here.

That’s it! You’re good to go. Your payouts should be coming in automatically and coded based on the mappings you set up.

Additional resources are always available for extra help and support wherever and whenever you need it.

Shopify Payment Processing Automation

Shopify payment processing used to be a bug bear for sellers.

To make their business lives easier and more streamlined, Shopify introduced Shopify Payments, or Shop Pay, as it is now called.

With the help of Stripe, Shopify allows sellers to keep all their payment information in their Shopify dashboard - with the option to extend to other providers if they wish to. This centralized system alleviates some of the previous pain-points experienced by Shopify sellers.

What does this mean for your Shopify QuickBooks integration? Simplicity and transparency.

If you can achieve the same high value output from less apps, you will ensure greater efficiency across your business operations. Save your additional app spots for ones that will offer you unique value.

Pro tip: You might think it wise to decide which payment processor/s to use based on the behavior of your consumers. This is not always the case - payment processors can be costly and time consuming so ensure you pick the right one for your business and operations.

For more details about Shopify Payments, check out our blog Why You Should be Using Shopify Payments.

How to Reconcile Shopify in QuickBooks

Your Shopify integration with QuickBooks Desktop and A2X will make your reconciliation process quick and pain-free. So, how do you do it?

This is how your Shopify payouts will look in A2X. We have highlighted the payout we will use in this example:


This payout matches the following shown in QuickBooks, ready to reconcile:


Within this payout, the following transactions have been captured by A2X (without A2X, you would need to calculate these manually):

A2X reconciliations

When this is sent to QuickBooks, it will appear as a journal entry:

Journal entry

When these arrive in your QuickBooks account, the transactions will be mapped out based on the tax mappings you determined in the setup phase. A2X is designed to make as much of the process as automatic and ‘set and forget’ as possible.

In the Banking section of QuickBooks Online, you will see that QuickBooks has picked up the transaction:


All you need to do is click “Match” to reconcile the journal entry with the deposit. The accounting for this payout is now complete. Easy!

This is how your completed payouts will appear in your financial statements:

Match transactions

As you can see, adding A2X to your accounting tech stack will save you huge amounts of time on manual calculations.

Almost all of the process is automatic, giving you the freedom back to focus on your business growth and easy access to accurate, up-to-date numbers when you need them.

For a step-by-step breakdown on this process for PayPal payments, check out this support center tutorial.

Inventory Management for Shopify

A2X has a feature built in called Cost of Goods Sold (COGS).

As your transactions come into A2X, this feature keeps track of what stock has sold and how much it cost you, enabling you to keep an overview of inventory levels and profit margins.

Ensuring that your inventory is healthy and that your items are profitable is key to understanding and growing your Shopify business. This is just another way that A2X helps ecommerce sellers to stay on top of the most important parts of their business.

To find out more about COGS and how to enable it in A2X, see our tutorial here.

QuickBooks Commerce for Shopify Sellers

An added benefit of using QuickBooks for your ecommerce store is that you will have access to a bundle price for the QuickBooks Commerce add-on.

QuickBooks Commerce offers QuickBooks Online users an extended service for ecommerce.

Its features include:

  • Order management to track and fulfil orders.
  • Inventory control across multiple channels.
  • Automated order and shipping workflows.
  • Custom reporting and insights.
  • Automatic listing of products across channels.
  • 1000 sales orders processed per month.
  • Wholesale options with customizable B2B stores.
  • Custom shipping rates across carriers.
  • Support for 2 sales channels.

QuickBooks Commerce allows you to automate more aspects of your Shopify store under the same roof as your accounts. This gives you visibility over a greater portion of your business in one place, helping keep your operations as smooth and digestible as possible.

As a QuickBooks user, you do not have to add QuickBooks Commerce onto your plan. You can use a combination of other apps to achieve the same functionality, but they may need to be connected externally to QuickBooks.

Find out more about this add-on here.

More Information About Shopify Accounting

Here at A2X, we love helping Shopify sellers succeed. Below are some of our in-depth guides on the various aspects of selling on Shopify to give you the tools you need in your journey:

Apps, Automation & Accounting

Increasing Traffic & Sales

Shopify Tax

Shopify Fulfilment

Shopify to QuickBooks Integration FAQs

Does Shopify integrate with QuickBooks?

Yes, it does. Shopify integrates with QuickBooks quickly and easily. See our steps above for how to do this.

Does Shopify integrate with QuickBooks Desktop?

Yes, Shopify integrates with all QuickBooks Desktop, Online and Enterprise. Check out our steps above to find out how.

These apps give you the option to link to each other from within their systems. Check out our guide above for the steps on how to do this.

How do I import sales from Shopify to QuickBooks?

When you integrate Shopify and QuickBooks, your sales will be imported automatically. The transactional data is fairly minimal without an accounting connector like A2X, which gives you the next level of detail that you’ll need to know for your ecommerce business.

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Start your free trial

Get accurate ecommerce accounting without the fuss with A2X. 

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