Best Accounting Software for Shopify 
Doing the books is not much fun for any Shopify storeowner.
But skipping the task is not an option. So, we need to make accounting and bookkeeping as painless as possible with the use of automation.
The two most popular accounting programs for small businesses are Xero and QuickBooks. Being able to sync transactions between Shopify and these programs does not happen automatically but can happen with the right app.
Fortunately, an entire community of apps has developed to help Shopify merchants make Xero and QuickBooks accounting simpler by automating much of the key work – and that’s what we focus on in this accounting apps review.
So, without further ado, let’s take a quick look at the five best accounting and bookkeeping apps for QuickBooks and Xero …
There are two apps of the same name – and both are included in this accounting apps review so careful not to get them confused.
First, the one by the team at Webgility. It allows you to sync orders, inventory, and fees to QuickBooks, Xero or NetSuite, keeping the books in order and providing visibility on cashflow.
This app is used by thousands of merchants on Shopify – and is one of the best-reviewed accounting apps out there.
Price: From $15/month (100+ orders and one sales channel) up to $299/month (500+ orders)
Free Trial? Yes – 15 days.
Average Shopify Rating (out of 5 stars):4.8 (545 reviews)
- Easily sync Shopify orders to Xero and QuickBooks Online/Desktop (and NetSuite in the more advanced versions)
- Sync daily summary or each transaction/settlement
- Live updates to your inventory with every Shopify sale
- Automatically create missing items for order-level tracking
- Keep bank deposits matched with accounts and sales taxes in order
- Gain insight into cashflow, revenue, expenses and performance
- Maintain compliance and an up-to-date inventory
- Sales tax compliance for single or multiple tax jurisdictions
- Helps you handle refunds and cancellations
- Record Shopify related fees as a separate bill transaction or as part of the original sale
- Unlimited support included in all packages
- Optional white-glove onboarding provided
- Excellent reviews from Shopify merchants
- Some users have difficulties setting up – but the support team is on hand to assist
- No free version
This is the “other” app of the same name. Created by the team at A2X, it is developing an equallygood name as its more established namesake and works with Xero, QuickBooks and Sage.
The price entry point is slightly higher but there is a generous 30-day free trial to compare it with other accounting apps reviewed here. It is trusted by thousands of merchants.
Price: From $19/month (up to 200 orders) to $99/month (up to 5,000 orders)
Free Trial? Yes – 30 days.
Average Shopify Rating (out of 5 stars):4.8 (100 reviews)
- Provides trusted and accurate financials
- Automates accounting for Shopify stores using Xero, QuickBooks and Sage
- Monitors your store, detects payouts, and posts sales/fees automatically to your accounting ledger
- Automatically reconciles payouts
- Provides full visibility of your Shopify sales and fees
- Helps with refunds or adjustments
- Posts accurate summaries to Xero, QuickBooks & Sage ledgers using the invoice API
- Loads past Shopify payouts, generating up to a year of financial history
- Can scale to support large stores as well as smaller stores
- Works whether you’re selling on one store or 100 stores
- The professional and advanced plans are reasonably priced
- Excellent reports about customer service
- Slightly higher price entry point for smaller stores than some other apps reviewed here
The Parex Bridge app is designed for Shopify stores using Xero as their accounting package – and may be a great option if you are just starting out in ecommerce or are beginning to grow.
The attractive pricing goes down well in the Shopify community, where Parex Bridge has become one of the best-reviewed Xero accounting apps.
Price: From $10/month (up to 100 orders) to $30/month (2,500 orders)
Free Trial? Yes – 7 days.
Average Shopify Rating (out of 5 stars):4.9 (105 reviews)
- Automatically syncs your Shopify data with a Xero online account
- Syncs all order information such as customer, line items, taxes, shipping, etc.
- Syncs automatically in real-time or daily – or you can do it manually if you prefer
- Manage prepaid orders and delayed-payment orders more effectively – the app syncs when payment is made
- Manage cancellations and refunds
- Tax and shipping lines synced to your Xero account
- Optional add-on that syncs inventory between Shopify and Xero
- Suitable for stores with customers in Australia, UK, US, NZ, South Africa, Ireland and Canada
- New features are regularly added by the developer
- Easy to install and use
- Good reports about customer support
- Short free trial – only 7 days
- Occasional problems reported with the inventory component
Bold Apps is a well-established developer with over a dozen available for Shopify merchants – most of which are extremely well-reviewed.
This one seems to have missed out on the positive reviews to date but we include it in this accounting app review as it is one of the few Xero-focused apps with a free version.
It can help you get to grips with tax and may be a great option for businesses starting out to consider. A lot of the criticism of the app occurred in its early days and many of the problems appear to have been ironed out.
Price: Free up to 30 orders/month. Paid plans between $19.99/month (200 orders) and $59.99/month (unlimited orders)
Free Trial? No
Average Shopify Rating (out of 5 stars):2.8 (185 reviews)
- Automatically export Shopify orders to Xero every day
- Each exported order from Shopify into Xero automatically includes all line items, shipping, and taxes
- Refunds, discounts, and payment fees are automatically recorded separately if you use Shopify Payments
- Can automatically import customer information along with your orders (optional)
- Receive daily notification emails
- Financial reporting possible in just a couple of clicks
- Integrates with global financial apps like TaxJar, Taxify, etc.
- Automatically sets up new tax agencies and their associated tax rate based on imported orders
- Set a primary tax agency for where you most regularly do business
- Run reports to see how much you owe in taxes
- Free version available
- Some technical/compatibility issues with app – but support has a good record of fixing issues
One of the best free accounting apps for Shopify stores using QuickBooks Online is this one by OneSaas.
By integrating QuickBooks Online with your store, it can save you hours of time from manually inputting bookkeeping data – and hundreds of favorable reviews suggest it does a great job of that. Not bad for free!
Free Trial? Not applicable
Average Shopify Rating (out of 5 stars):4.7 (342 reviews)
- Integrates QuickBooks Online seamlessly with your store
- Saves you time by automatically sharing data between Shopify and QuickBooks
- Can connect multiple sales channels to QuickBooks ensuring stock levels are up-to-date
- Reduces human error from manual data input of invoices, customers and products
- Helps you update stock levels between QuickBooks Online and Shopify
- Share updates/created products from Shopify to QuickBooks Online
- Share when an order is made in Shopify and create or update the sales invoice or receipt in QuickBooks Online
- Support provided
- Integrates with Mailchimp
- Completely free – no paid versions available
- Some disgruntled MYOB users, which used to be supported by the app (no longer)
- A few historical technical complaints – but support seems responsive and it’s FREE
Best Shopify Accounting App
Next time you’re groaning about getting your Shopify store’s accounts up to date, think of the above apps. It might be time to try one or two of them to make life easier.
After all, you should be spending less time on the books and more time on growing your business.
The reviewed apps can help you do that, streamlining your back office and doing what used to take hours in a matter of seconds.
They can help make end-of-month headaches a thing of the past as bank deposits, accounts and sales taxes are all reconciled, in good order, and ready to file.
If you use Xero or QuickBooks and run a Shopify store (or two), these apps could be just what you’re looking for to automate your accounting and keep your finances in order.