8 Best Shopify Accounting Apps (Which Do We Recommend)

Running a business is no walk in the park. It becomes even more complicated when you’re handling the accounting yourself. 

Accurate accounting is vital to growing your business and ensuring its success.

Luckily, technology is a valuable tool that can make everything a lot easier, even businesses accounting!

There are hundreds, if not thousands, of Shopify accounting apps that ‌help you run your business and save you both time and money. 

We’ve researched the 8 best Shopify accounting apps and will even recommend the best app in this guide. 

Our guide will ensure that you won’t have to do hours of research to find the best Shopify accounting app for your business.

How To Choose The Best Shopify Accounting Apps?

Before we jump in, let’s take a step back and think about what you should look for when choosing a Shopify accounting app. 

There are many apps out there. They all promise to help streamline your accounting and increase your profits, but not all of them live up to their promise. 

So, it is essential that when choosing the best accounting app for your business, you consider:

  • Platform integration: The accounting app you choose should be able to seamlessly integrate with Shopify and any other apps you’re using. These other apps could be shipping, reconciliation, or print-on-demand apps. Having this feature will make running your business much more manageable!
  • Sales tax configuration: Taxes are a headache! Even more so if you’re a business owner. So, you must choose accounting software that makes calculating, collecting, and paying your taxes as easy as possible! 
  • Customer support: Not all of us are as tech-savvy as we want, especially when learning new software. So, when looking for an accounting app, finding one that offers fantastic customer service is a must. Preferably, ‌find one that offers 24/7 support options. This helps navigate different time zones and ensures that you can find help whenever needed. 
  • In-depth reporting: Most accounting apps offer basic account reports. While this is fine for most, in-depth accounting reports are a must if you’re planning on expanding your business! It helps you keep track of your expenses and profits. It could also offer valuable insight into market trends and which products perform better than others. 
  • Affordability: No two businesses are the same. They’ve all got different budgets and can afford different tools. When looking for the best Shopify accounting app for your business, you need to consider its affordability. There’s no point in paying for an expensive accounting app if it'll drastically reduce your profits.

Finding an accounting app that works for you can be stressful, even with the help of these handy tips. Luckily for you, we’ve listed our favorite Shopify accounting apps right here! 

Ultimate Review Of The Best Shopify Accounting Apps


Freshbooks is one of the most popular accounting apps around. 

Freshbook offers essential accounting functions like charting accounts, journal entries, and bank reconciliation to items.

What We Like

Freshbooks has a great project tracking feature that lets you split your projects’ expenses. This feature is beneficial when figuring out which products and projects are viable and which aren’t. 

You can also use this feature for tracking valuable performance indicators, such as profit margins and targets.

The greater your overview of what works and what doesn’t work in your business, the easier it becomes to improve your business.

Another vital feature that Freshbook offers are their tax categories. Tax categories help users prepare and file their taxes without taking too much time. 

Freshbooks also supports over 170 currencies, making it a fantastic choice if you have international clients. 

The app is available as a web application or a mobile app on Android and iOS. 

What We Don’t Like

Freshbooks may seem like a fantastic app. However, it is not without its downsides. 

The first downside is that it is a paid app. While a free trial is available if you’d like to test it out, the paid plans start at $4,50 per month. 

The app also has a few odd restrictions. For example, each plan supports a single user, and it costs a fair bit to add more to the platform. 

Overall, Freshbooks is a fantastic app for individual business owners looking to expand!


Much like Freshbooks, QuickBooks is popular with small business owners and freelancers. 

This accounting app can track orders, track your income, signal material availability, and create customizable invoice templates. 

What We Like

Besides some fantastic accounting features, QuickBooks also helps track your bank account balance, cash flow, vendor bills, and the cost of goods sold. 

QuickBooks is a real winner in that you can easily integrate it with many platforms like Shopify, Amazon, PayPal, and Square. 

The app offers four plans, each with its specific features.

 It is also available as a mobile app on both Apple and Android devices. Since it is a mobile Shopify account app, you can also get real-time reporting. 

The mobile accounting app is excellent if you have a busy lifestyle and are always on the go. 

What We Don’t Like

The only downside to this app is that it is an additional expense. 

QuickBooks plans typically start at $15, making them much more expensive than Freshbooks. Besides this, some vital features like the project management tool are hidden behind a paywall. 

However, if you have some cash you’re willing to spare, this app is excellent for business owners with hectic, on-the-go lifestyles. 


Xero is by far one of our favorite Shopify accounting apps. Xero offers both a web and mobile app and supports Android and iOS for convenient access. 

What We Like

The Xero accounting app provides an extensive array of accounting features. 

One of our favorite features is the innovative contract management feature. This feature makes it easy to merge your finances, marketing, and comprehensive reports in one easy-to-access place. 

Xero also offers over 65 different reports. For instance, Xero can provide reports like P & L, balance sheets, and equity reports. You can easily customize all of these reports to suit your preferences. 

Unlike Freshbook, Xero offers unlimited users and is scalable to suit your business needs. 

What We Don’t Like

You have to manually find and match transactions in Xero and create invoices for some gateways to account for the fees, even when setting up rules.

Luckily, Xero works perfectly with our tool, Reconcilely!

By using Reconcilely and Xero, you can automatically send Shopify payments, refunds, and fees from any payment gateway in real-time. 

The app is super easy to install and user-friendly! It’s easy to see why Xero is a favorite of ours. 


NetSuite is one of the top Shopify accounting apps around. It offers everything a business owner could want and lets you oversee most of your business’ finances without issue. 

What We Like

NetSuite has some key features, including automating your financial management, inventory management, billing, and customer orders!

Automation can save you a ton of valuable time and money. 

NetSuite also offers many features and custom accounting tools at the enterprise level. 

These features allow you to have more control over your accounts. It includes features like fixed asset management and a fancy tax engine that takes care of all your domestic and international sales tax compliance. 

What We Don’t Like

However, the one major downside to this all-inclusive app is the cost. NetSuite is by far the most expensive app on this list. At around $999 per month, it breaks the bank. 

Still, NetSuite is an excellent app for established business owners looking for an upgrade to their current Shopify accounting app. 

Sage Business Cloud Accounting

Sage is a fantastic, affordable Shopify accounting app. It is a web-based and mobile application (Android and iOS) and offers new users a free trial if they’d like to check it out before the purchase. 

What We Like

What makes Sage a genuine contender is its time-saving features. 

For example, Sage offers automatic transaction matching. Transaction matching means you can connect your bank account to the app. The app will use specially designed AI to memorize all your categorization choices. 

Sage also offers gorgeous custom invoice reporting and is visually beautiful. If you’re a sucker for aesthetics, this might be your app. 

Besides all this, Sage also offers a remarkable in-depth reporting feature for monthly, quarterly, and annual financial reports and is highly customizable. 

What We Don’t Like

Sage doesn’t offer a free trial period. It also has no favorites options for your debtor or creditors list reports. The lack of this feature makes reporting a tedious process if you have many debtors and creditors to work through.


Wave is one of the few exceptions. It is a free Shopify accounting app. Now, we know what you’re thinking, but just because it’s free doesn’t mean it isn’t able to stand among the other apps on this list. 

What We Like

Wave is perfect for newbie business owners looking for a budget-friendly tool. It is super fast to set up, and it also allows you to connect multiple businesses to the app. This feature is excellent if you’re running more than one online business and are looking to streamline your accounting process. 

Besides this, it is also super easy to link your bank and credit cards, and it offers PayPal integration. 

Since Wave is available as both a web-based and mobile app (Android and iOS), you can access your accounting app from anywhere globally, as long as you have a reliable internet connection.

Wave also offers new users a free trial if you want to try it before committing. 

What We Don’t Like

Unfortunately, you cannot connect to other payment systems like PayPal or Stripe with Wave. You’ll have to use their payment platforms for processing any payments.

Overall, Wave is an excellent Shopify accounting app if you’re starting and looking to save some cash. 


Botkeeper is an accounting app that offers the full suite of features needed for you to automate your accounting and finances. It has a stunning, user-intuitive dashboard that provides data visualization, financial data sets, trending analytics, and KPI tracking. 

What We Like

The app also offers a handy document manager, which allows you to store important financial documents online. 

Botkeeper offers detailed financial reports and can automate specific accounting tasks, such as billing and customer orders. 

What We Don’t Like

Much like Freshbook and Sage, Botkeeper is a paid application. Plans begin at around $79 per month. 

Botkeeper is an excellent app for small business owners to simplify their financial processes. 

Versa Cloud ERP

Unlike most of the apps on this list, Versa is a fully online web application. Versa is perfect for working with an international client base since it offers multi-currency support. 

What We Like

The app offers everything you’ll need to manage your business finances, such as selling, inventory, returns and refunds, and dropshipping. You can access these features on the handy, intuitive dashboard for easy access. 

Versa also offers fantastic customer support that is available 24/7. 

What We Don’t Like

As with most apps on this list, Versa is a paid app. It costs around $99 per month for a membership plan. 

Overall, Versa is an excellent option for businesses with an international clientele. 

Use The Best Shopify Accounting App

Finding the perfect Shopify accounting app to suit your business needs can be challenging, especially if you’re pressed for time. Luckily, your job just became much easier with our list of the best Shopify accounting apps!

We recommend you check out Xero. At Reconcilely, we’ve worked with Xero for several years and can vouch for their efficiency, reliability, and reputation. 

What’s more, our Reconcilely app works perfectly with Xero to streamline your financial processes! 

Using these two great apps together, you can easily simplify your accounting and automate daily accounting tasks.

You’ll save valuable time and will find that it’s easier to stay in control of your business finances. Being an online success has never been easier.

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