Back Compliance

How to Integrate Your Accounting Software with Shopify—Full Guide

Julia RichardsJune 2021
How to Integrate Your Accounting Software with Shopify—Full Guide


Shopify has completely revolutionized e-commerce. Unlike its competitors — WooCommerce, Wix, Squarespace — Shopify stands out from the rest in that it is entirely and completely built around e-commerce only. Instead of being a plugin or add-on, it is the shop and website your e-commerce business runs on.

Other tools provide e-commerce as an additional functionality or added plugin. Shopify is e-commerce, and everything about the service is dedicated to getting your business up and selling within minutes.

Plans for Shopify

The pricing is highly competitive and scales as your business scales so that you only pay for what you need.

Plans for Shopify start from as little as USD29.00 a month for sellers who are new to e-commerce.

With just a few clicks, a person can get their e-commerce store going in no time, which makes Shopify an extremely popular choice for e-commerce businesses, powering upwards of 1,000,000 e-commerce websites!



Why is it important to integrate Shopify with an accounting tool?

Whether you’re using Shopify or some other e-commerce system, integrating that system with your backend accounting system is essential to your own sanity; particularly if you’re selling in large volumes.

The reasons for this are as follows:


Bookkeeping will be a nightmare

Export to CSV

Without integrating Shopify with your accounting system, you will need to keep up your bookkeeping manually. Shopify provides an “Export to CSV” option, and the resultant CSV file is massive.

Manually inputting all that exported data into your bookkeeping system is a potential minefield of errors.

If you’re using Excel for your accounting, you might be able to write some macros to get the data imported automatically, but that’s starting to get really complicated!

Most businesses these days use online accounting and bookkeeping software. If you’re a small business, some of that software is even available for free, such as Wave Accounting.

But, whereas accounting and bookkeeping software can save swathes of time once the data is in the system, it can potentially add time if you have to import a lot of data from a CSV file. Often, the CSV file needs to be formatted in a particular way. This requires more of your time and opens the door to even more potential errors.

In short, connecting Shopify to an online accounting system is imperative for peace of mind, so you can simply work on your business and let the bookkeeping take care of itself.


Shopify fees

The problem is made more complex when one adds Shopify fees to each transaction. In some cases, Shopify will charge a small fee per transaction. In your accounting, you could add this as a tax-deductible expense. Manually sifting through fees or figuring them out in an exported CSV file further adds to the potential of human error when updating your bookkeeping software manually.

Shopify fees

What are the basic requirements to connect Shopify with my accounting software?

Fortunately, Shopify connects with many accounting systems to keep the two systems in sync, and automatically update your bookkeeping.

Essentially, the main criterion required to connect your accounting software to Shopify is that a “middleware” app has been specifically designed to do this.

Most of these apps connect to online accounting services. But there is also a connection for QuickBooks Desktop which can be obtained in the Shopify app store.

If a tool doesn’t exist in the Shopify store or made by the accountancy software provider itself, sometimes tools like Zapier can help connect that particular software to your accounting system, but that starts getting a little more complex.


How to integrate FreeAgent with Shopify

FreeAgent is an extremely popular accounting tool, especially amongst solopreneurs, freelancers, and sole proprietors. It is also very popular with other small businesses.

the FreeAgent App page

The only drawback to this integration is that it only works with UK VAT rates. So, if you’re selling using another country’s VAT Rates, you won’t be able to use the plugin.

The plugin works by importing the data daily to FreeAgent.

FreeAgent then automatically generates invoices for any items sold.

FreeAgent connects directly with Shopify. All that is required is to visit the FreeAgent App page on the Shopify Plugins store and then add the plugin to your Shopify store.

Simply click the “Add app” button to begin the integration.

If you are not logged in, Shopify will prompt you to log in.

You’ll be asked to confirm the connection, and to review the various permissions that are required for this integration:

confirm the connection

You will then be taken to FreeAgent’s website and asked to log in.

On FreeAgent’s page, you will be asked to confirm that Shopify can access your FreeAgent data:

confirm that Shopify

After accepting all the permissions, you’ll be taken back to Shopify’s page to configure all the settings so that FreeAgent knows how to handle any purchases made.

These configurations include:

  • Setting the date to start the configuration from
  • Setting up the VAT rates and sales categories
  • Reviewing the contact name to use for any invoices created in FreeAgent
  • Specifying the spending categories for Shopify fees and card fees
  • Confirming that you don’t have foreign tax rates applied.

And, voila! Your data will be automatically imported and synced!


How to integrate QuickBooks Desktop with Shopify

How to integrate QuickBooks Desktop with Shopify

QuickBooks Desktop can sync with Spotify using the QuickBooks Desktop plugin available in the Shopify App Store.

All order information from Shopify is synced once a day, and all information is pulled into QuickBooks Desktop, including customer details, line items, taxes, shipping, etc.

The tool has the added benefit of handling multi-currency orders without a problem. And it can also sync data from multiple Shopify stores into one QuickBooks Desktop file for syncing.

To connect QuickBooks Desktop to Shopify, visit the plugin page above, install it, and then follow the prompts.

It should be noted that the syncing tool provided here is not made by QuickBooks, but by a third-party company called Parex Technologies.


How to connect QuickBooks Online with ShopifyQuickbooks App page

QuickBooks also doesn’t provide an in-house solution to link Shopify with their accounting software. So, again, we’ll have to resort to third-party solutions.

There are several on the market.

One of the solutions can be found on the Intuit (the makers of Quickbooks) App page, made by a company called Bold Commerce. Unfortunately, this particular app has some pretty dismal reviews, so we’re not going to recommend it.

On the Shopify app store, however, there’s an app by Parex, which also makes the QuickBooks Desktop Sync tool for Shopify.

Parex’s QuickBooks Cloud sync tool has excellent reviews:

Parex’s QuickBooks Cloud sync tool has excellent reviews

The app costs USD10/month, with a 7-day free trial.

Adding the app follows a similar procedure compared to the first one we covered (FreeAgent). You will be prompted to grant the appropriate permissions on both websites (QuickBooks and Shopify), and then you’ll need to configure how you want Shopify’s data to be pulled into QuickBooks.


Other providers to connect QuickBooks Online to Shopify

As with all tools created by third parties, you’ll have to make a call as to which one you want to use.

Here are some other options for connecting QuickBooks Online to Shopify:

How to connect Xero with Shopify

Xero also does not provide its own in-house connection to Shopify, but it does recommend some apps on its webpage that can do the job.

How to connect Xero with Shopify

The three recommended apps to connect Xero to QuickBooks are:

All of the apps have incredible reviews (4.8 to 4.97 stars).


A2x for Shopify

A2x for Shopify automatically posts Shopify data to Xero. It reconciles payouts, fees, refunds, and adjustments so that these don’t need to be entered manually.

To get started, visit the A2x website, open an account and then install the app. They have a free trial period for you to test the app.




Amaka summarizes all daily transactions from Shopify into one invoice and automatically categorizes and groups those transactions to make use of Xero’s powerful reporting capabilities. The tool also takes care of payment fees and taxes.

To get started, you will first need to create an account at Amaka.

Then click the New Integration button.

There will be several authentication and permission screens that follow, both for Shopify as well as for Xero. You will need to grant permission for the Amaka app to access your Shopify account as well as your Xero account.

After clicking Save + Continue, the integration is live and ready to start syncing!


Parex Bridge for Xero

Parex Bridge provides daily syncing between Shopify and Xero. It syncs Shopify orders, products, and customers.

You can configure Parex Bridge to run entirely automatically, or choose a manual option so that it runs only when you trigger it through the click of a button.

Refunds and order cancelations are all dealt with by the app. Partially paid orders are also handled appropriately. Customers can be imported individually, or you can choose for them to be synced to a single customer such as “Shopify.”

The tool also deals with Tax and Shipping costs appropriately.

To configure Parex Bridge for Xero, visit the Parex Bridge page on the Shopify App Store and click “Add App.”

Parex Bridge for Xero

If you are not logged in to Shopify, you will be prompted to log in.

Like all the other apps in this article, you will need to authenticate and accept permissions as necessary, both on Xero’s side and Shopify, so that the two systems can communicate with each other.

Once you have authenticated, you will be prompted to fill in some settings, such as the Xero account you want to log Shopify purchases in, how to handle Gift Card purchases, and any Xero prefixes you want to use if you are connecting more than one Shopify store to Xero.Shopify store to Xero

There are also options to configure how to handle Shopify PayOuts and how to handle Xero products when syncing orders.Shopify PayOuts

You will then need to select the package that matches your needs:

select the package that matches your needs

The available packages for Parex Bridge for Xero are:

  • Silver – USD10.00/month, for up to 100 orders a month.
  • Gold – USD20.00/month, for between 101 and 1,000 orders a month.
  • Platinum – USD30.00/month, for stores with up to 10,000 orders a month. (You will be charged an additional USD10.00 for every additional 5,000 orders.)


How to integrate FreshBooks with ShopifyHow to integrate FreshBooks with Shopify

Like FreeAgent, FreshBooks has created its own app to connect directly with Shopify. Unfortunately, it does not have great (or many) reviews.

The app can be installed directly from the Shopify App Store.

Also, like the FreeAgent app, this one doesn’t cost anything (although you do need a FreshBooks subscription to use FreshBooks).

To install, click Add App from the Shopify page, authenticate, and accept the permissions on both Shopify and Freshbooks for the app to access your accounts.

The app gives you several options when syncing client data. These are:

  • Syncing orders to a new client with the name “COMPANY+NAME”
  • Syncing all orders to an existing client
  • Creating a new client for each order processed

You can see these options below.syncing client data

The screenshot above also shows the option to sync data on a schedule, or every time you click the Sync Manually button.

For every order in Shopify, an invoice is generated in FreshBooks. Inventory data is pulled from Shopify, and the Shopify products will be considered the Master Source of data. Which will then update/modify FreshBooks’s data These products can be synced manually or automatically with FreshBooks.


How to integrate Wave Accounting with Shopify

How to integrate Wave Accounting with Shopify

Wave’s free accounting software is only available to US and Canada-based customers. Unfortunately, Wave’s in-house Shopify syncing feature came to an end on Dec. 31, 2020.

But there is still an app on the Shopify App Store called “Sync to Wave.” This app is not reviewed by Wave itself, and it has very few reviews. (And the reviews are not great.)

To connect this tool, click Add App, authenticate and accept the required permissions, then configure the settings.

Sync to Wave offers the following functionality:

  • Sync orders from Shopify to Wave as accounting transactions.
  • All line items, shipping fees, and applicable taxes are synced.
  • Any new sales taxes created in Shopify will be automatically added to Wave.
  • Gift card payments can be synced.
  • Shopify PayOuts can be synced.
  • The app also supports multiple stores.

Another option for Wave syncing with Shopify is Zapier. But this requires a lot more individual setup compared to a dedicated app.

Wave syncing with Shopify is Zapier

How to integrate Zoho Books with Shopify

Zoho Books connects to Shopify by means of its in-house integration platform, Zoho Flow.

The major drawback with it is that it requires configuring each aspect of Shopify to Zoho Books, rather than being a one-click, “black box” solution that takes care of everything for you.

Although the potential of this integration method is vast, we feel that the setup is clunky. Also, the Standard tier of Zoho Flow—USD10/month—is limited in the number of actions it can carry out a month before you need to upgrade to a higher tier. That higher tier is a whopping USD24/month which we felt was a little hefty if all you want to do is integrate Shopify with Zoho Books and not use any of Zoho Flow’s other features.

Zapier is another option when it comes to integrating Zoho Books. But that has similar issues to Zoho Flow, because both those services are an all-in-one integration service, and not “Black Box” services which take the complexity out of connecting Shopify to an accounting system.

Overall, we were disappointed with Zoho Books’s offering.


Which is the best accounting software to integrate with Shopify?

Based on the above factors, we gave each of the accounting tools above a star rating out of five according to how we felt they dealt with integration.

We compared all factors, including:

  • Pricing
  • Reviews from users
  • Functionality

FreeAgent lost points because:

  • The reviews are bad
  • They only support UK tax, which really sucks

FreshBooks equally lost stars because of the negative reviews.

Wave only has a third-party app and the reviews are not great.

We felt Zoho was too complex to be user-friendly, and too expensive.

We’re not fans of Desktop apps, but we couldn’t find anything that worked against QuickBooks Desktop, so it also gets a five-star.

Xero is the clear winner, though, with some excellent third-party tools that are highly reviewed and extensively used. (We gave it a bonus star.)

Here’s our subjective review of how well each of the above accountancy tools integrates with Shopify:




QuickBooks DesktopQuickBooks Desktop


QuickBooks DesktopQuickBooks Online

Xero logoXeroFreshBooksFreshBooksWaveWaveZohoZoho
App available?

(several apps available)

Built in house?
Has all major features?
Good reviews?

(excellent and many reviews)

Overall Rating★★★★★★★★★★★★★★★★★

Bonus star:


About author
Julia Richards
Julia Richards

Our head of content, Julia has spent the past 20 years assisting entrepreneurs with all aspects of business launch and growth strategies in various industries around the globe.

Other Blogs Might Interest You

How to Integrate Your Accounting Software with Shopify—Full Guide
Compliance How to Integrate Your Accounting Software with Shopify—Full Guide

  Shopify has completely revolutionized e-commerce. Unlike its competitors — WooCommerce, Wix, Squaresp…

Julia Richards June 2021
All the Essential Business Software Your Small Business Needs
Operations All the Essential Business Software Your Small Business Needs

Doing business in today’s world without utilizing any software is like trying to drive without wheels. Autom…

Julia Richards June 2021
4 Most Business-Friendly States in the USA to Form an LLC in 2021, Compared
Compliance 4 Most Business-Friendly States in the USA to Form an LLC in 2021, Compared

In any “best of” survey, it’s important to remember the factor of weight variables. Every person’s cir…

Julia Richards June 2021