Best Shopify Accounting Software

Are you looking for the best Shopify accounting software? Shopify is one of the most popular eCommerce platforms on the market. But you probably already know that and that’s why you want to find the best Shopify accounting software you can to combine and automate many of your daily tasks…right?

Well, that’s what we are here to help you with. We have compiled some of the best Shopify accounting software options, so you don’t have to spend endless hours looking at and researching which one might be best for you.

Let’s get started. We want to help you find the best possible accounting software for your particular situation. 

Here are what we believe to be the best Shopify accounting software platforms for eCommerce businesses.


Flowify is an exceptional Shopify accounting app. Flowify will integrate all your sales, refunds, fees, bank deposits, and more seamlessly into QuickBooks. This app will streamline the accounting process so you can automate all your accounting to QuickBooks. Using Flowify will allow you to spend time on other income-producing tasks rather than on accounting. Flowify is quickly becoming the best Shopify accounting software for eCommerce businesses.


QuickBooks is one of the most recognized accounting software platforms on the market. QuickBooks has plenty of features, including the ability to connect your bank accounts, third-party apps, and QuickBooks Payroll. It also allows you to track your orders, manage inventory, and material availability. And, unlike FreshBooks, QuickBooks doesn’t charge you extra for each additional user. However, some people find QuickBooks a bit difficult to learn.


FreshBooks is a great time-saving cloud-based software. Its main features include automated bank imports, unlimited expenses, built-in tax categories, bank reconciliation, tax-time reports, and more. FreshBooks also provides you with easy-to-understand business and performance reports. However, FreshBooks requires you to pay monthly for each additional user aside from yourself. This can really add up if you have a medium or large team. And, on top of that, FreshBooks is a bit pricier than other similar accounting software programs.


Xero includes 800 integrations for eCommerce businesses of all sizes. It comes with transaction reconciliation, bill and receipt capture, cash flow, expense claims, payroll, and more. However, if you want unlimited bank transactions, you will have to upgrade to a higher-tier plan. Additionally, Xero doesn’t offer live customer phone support. So that’s something to consider.


Wave is free cloud-based accounting software that will track your income and expenses, has receipt scanning, will organize your financials, bank reconciliation, and will create your invoices for you. This option is good for small businesses that only need a simple platform without a lot of bells and whistles. For example, there’s no detailed mobile app. It only comes with an invoicing and receipt scanning app. And, Wave doesn’t have the reporting features and customization options that are commonly available with other accounting software programs.

Sage Accounting

Sage is highly customizable accounting software that will connect with your bank while using AI to memorize your categorization options. The Sage platform is extremely user-friendly, comes with industry-specific features, a powerful inventory reporting feature, detailed reporting, budgeting, automated workflows, auditing, cash flow forecasting, and more. Sage is a great option due to its abundant time-saving features.


NetSuite is great, especially for large businesses. With NetSuite, you can automate your order, billing, inventory, and customer features. And you can sync real-time customer and order information using custom triggers. Then you can sync and manage your inventory based on that information. NetSuite also provides reporting based on customer purchasing history and other buying behaviors, as well as automating your account receivables and payables. It also handles global and domestic sales tax compliance and more.

However, NetSuite is quite expensive. Therefore, unless you are a company with a large budget and are able to afford this helpful but expensive program, you might want to look for a more affordable solution.


Bench is a hands-off accounting solution. It is an online bookkeeping service with all the accounting functions being performed by humans with Shopify experience. Additionally, along with using humans, Bench also uses an artificial intelligence accounting element. Bench will provide you with a dedicated bookkeeper along with a team of experts. Your team will import your bank statements, credit card accounts, categorize your transactions, and prepare all your financial statements each month. Bench also supplies you with a variety of helpful reports as well. And while you have access to Bench bookkeepers, their response times often lag. Additionally, the learning curve can be challenging to some.

Zoho Books

Zoho Books is a scalable accounting app that will automate your complex business workflows quickly and easily. It allows you to set a trigger, add your actions, and use delays and decisions to create a customized workflow. It’s an end-to-end system that handles everything from the start of a transaction through to the invoicing. Zoho Books also has a team collaboration feature, so everyone can work together on the Zoho platform. Additionally, Zoho Books comes with a wide variety of features, and yet it’s extremely affordable. And most people find the Zoho Books platform easy to use.

What’s Next?

If you want a cloud software application that connects Shopify with cloud accounting, Contact Flowify today. We automate the bookkeeping for your Shopify store transactions, as well as your Shopify bank account reconciliation amounts. Flowify will save you time and money every day, every month, and every year. So why not sign up for the Flowify 30-Day Free Trial today?

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