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The Best Shopify Accounting Software: Our Top Seven Picks

Thanks to Shopify, 1.75 million business owners are making money online selling physical and digital products. If you’re among them, having an efficient, accurate Shopify accounting solution is crucial both for IRS compliance and a clear picture of your company’s financial health.

As one of the biggest ecommerce platforms, Shopify has some great built-in features to get you started, but their financial reporting has a few limitations.

For one thing, not all Shopify reports are available to store owners on all plans. That means that if your business isn’t quite big enough to justify paying for a higher-tier plan, you may be in the dark about some of your financials.

For example, although Shopify’s basic plan offers finance reports and limited access to inventory reports, it doesn’t include sales and profit reports. As your business grows, you’ll probably want to look into accounting software that can help you plan for the future.

Luckily, many robust accounting solutions integrate with your Shopify store. (In fact, the last time we searched “accounting” in the Shopify App Store, there were more than 1,300 results!) There are options out there, but choosing the right one can be tricky. So how do you know which ones are any good?

To make the choice easier for you, we’re sharing our top seven picks and the criteria we used to select them.

What does the best accounting software for Shopify have?

The best accounting solutions for Shopify have several things in common. They’re:

  • Easy to integrate with other tools: In addition to integrating seamlessly with Shopify, your software should play nice with other ecommerce tools you use, like order shipping apps and payment processors.

  • Cloud-based: Cloud-based solutions offer convenient access to your up-to-date data across devices and reduce the errors that sometimes happen when trying to sync information manually.

  • Able to meet current and future reporting needs: A good Shopify accounting solution has the detailed reporting capabilities you need now, but it should also be able to scale as your business does.

  • Easily accessible on all devices: All of the options below have, at the very least, a web application and mobile apps for Android and iOS devices.

Here are seven solutions that tick all of those boxes.

Best Shopify accounting solutions

  • Best free accounting software: Wave Accounting
  • Best time-saving software: Freshbooks
  • Best user-friendly solution: QuickBooks Online
  • Best for automation: Holded
  • Best for large enterprises: NetSuite
  • Best for integration selection: Xero
  • Best hands-off accounting solution: Bench

1. Best free accounting software

Wave Accounting

If you’re not looking to spend a ton on accounting software and your business is still small, Wave Accounting may be a good option for you. It’s free, easy to set up and use with little to no accounting knowledge, and easily accessible online and via its mobile app (for Android and iOS).

Pros

Wave accounting integrates with Shopify, of course, and can also connect to your bank accounts. This makes it easy to keep track of income and expenses, as does the ability to scan and add receipts to your records. Wave also includes a payroll management functionality for employees and independent contractors.

Plus, with Wave, you have access to a variety of helpful financial reports. These include profit and loss statements, cash flow and sales tax reports, Invoice by Customer reports, a Purchases by Vendor overview, and an Aged Payables and Aged Receivables report.

Cons

While Wave is a straightforward solution with sufficient functionality for most ecommerce businesses, other software offers more in-depth reporting and flexibility, which you may need as your Shopify store grows.

Additionally, Wave’s mobile app doesn’t offer all the features available on the website: it’s limited to invoicing and receipt scanning. If you’re dead set on accessing your financial reports from a phone or other mobile device, one of the other options we’ll cover may be a better fit.

Pricing

As mentioned, this software is free, although there are paid add-ons that might be of interest. These include:

  • Monthly bookkeeping and payroll support starting at $149 per month

  • Tax service starting at $1500 per year

  • Accounting and payroll coaching sessions for $229 each

Best For: Ultimately, Wave is best for small businesses that need a simple, affordable solution.

2. Best time-saving software

Freshbooks

Freshbooks—another cloud-based solution available on the web, Android, and iOS—makes a bold claim. The company estimates that businesses can save up to 192 hours per year by using its software. What features make this possible?

Pros

Freshbooks has all of the main features a Shopify store owner might need, including automated bank imports, bank reconciliation to maintain accuracy, a chart of accounts, built-in tax categories, tax-time reports, and unlimited expenses.

Freshbooks’ easy-to-understand business health reports and performance dashboards present your financial data in a way that gives an accurate, comprehensive picture of how your business is doing. If your work is project-based, you can even use Freshbooks’ handy project management tools to stay on top of deliverables.

Why is Freshbooks good for Shopify sellers specifically? It pulls information about the items, invoices, and payments related to your orders directly from Shopify, where you can view it along with the additional financial context Freshbooks provides.

Cons

One disadvantage of this tool is that you have to pay monthly to add users besides yourself to your account. While $10 per month per user isn’t expensive in itself, that cost could add up if several team members need access.

Additional features and services, such as a dedicated account manager, data migration services, and payroll, are only available as add-ons or as part of the higher-tier plans.

Pricing

Speaking of Freshbooks pricing plans, you may be interested in:

  1. Lite: $15 per month for basic features such as tracking unlimited expenses, client account statements, credit card payments, and US bank transfers.

  2. Plus: $25 per month for automatic expense tracking, recurring billing and retainers, business health reports, and the option to invite your accountant.

  3. Premium: $50 per month for project profitability tracking, bill payment and tracking, accounts payable, and so on.

  4. Select: Custom pricing for unlimited billable clients and specialized features that include a dedicated account manager.

If you’re not sure which plan would be the best fit, you can unlock all features free for 30 days (no credit card required).

Best For: Freshbooks is best for micro and small businesses that want to start simple and scale over time.

3. Best user-friendly solution

QuickBooks Online

QuickBooks Online, which is available as a web, desktop, and mobile application, is one of the most popular bookkeeping and accounting tools around. It’s a great option for Shopify store owners specifically because of its user-friendliness. You can set up your QuickBooks Shopify integration within minutes!

Pros

In addition to its Shopify integration, QuickBooks also allows you to connect your business bank accounts and third-party apps like Square, Stripe, and PayPal, as well as QuickBooks Payroll. With it, you can also track orders and material availability, as well as manage inventory.

In other words, QuickBooks serves as a central hub for all of your financial data, offering detailed reports ranging from profit/loss statements and expense reports to balance sheets and cash flow reports.

Plus, unlike Freshbooks, you can add and manage the permissions of several users at no extra cost. The basic plan allows access to one user and one accountant, and each of the other plans allows for more users.

Cons

QuickBooks is a robust and cost-effective solution, but it comes with a fairly steep learning curve. When you factor in the value of your time and the potential for error, that cost goes up quickly.

Learn more about Bench vs. QuickBooks.

Pricing

QuickBooks has four monthly plans:

  • Simple Start - $25 per month for basic features such as income and expense tracking, invoicing, general reports, and sales and sales tax tracking.

  • Essentials - $50 per month for everything in Simple Start, plus up to three users, time tracking, and bill pay.

  • Plus - $80 per month for everything in Essentials, plus up to five users, inventory tracking, and project profitability tracking.

  • Advanced - $180 per month for advanced features, including up to 25 users, automation, a dedicated accounts team, and exclusive premium apps.

If you want guaranteed accuracy, you can also add on live bookkeeping (monthly or one-time) and save yourself even more time.

Best For: QuickBooks is best for small businesses that need financial data from several tools pulled into one place.

4. Best for automation

Holded

Next up is one of several business accounting solutions that Shopify itself recommends—Holded. It’s available both as a web application and a mobile app (for Android and iOS). While not as well-known as some of the other names on this list, more than 80,000 businesses enjoy the robust set of features offered by this tool.

Pros

As far as Shopify is concerned, Holded has two main functions. One, it syncs Shopify sales with the rest of your accounting (and allows you to sort by sales channels). Two, it allows you to receive and manage Shopify orders in Holded and convert them into invoices.

Got more than one Shopify account? Connect them all for well-rounded, real-time insights into your business’s finances, from forecasting to in-depth accounting histories.

Holded also offers receipt scanning for recording expenses, cash flow reporting, remittances, payroll management, and more.

Cons

Most of this company’s big competitors include some form of receipt scanning in their monthly pricing, but Holded charges 0.20€ (approximately 0.25¢) per scan, along with monthly fees for its pro inventory management package, adding team members, and catalog management.

Additionally, tax filing assistance is only available in Spain. If that’s something you’re interested in, you’ll have to search for a tax pro that can help (or choose a solution that includes this service).

Pricing

While Holded has four plans, the three that include accounting capabilities are:

  • Standard - 49€ (approximately $57) per month for basic inventory management, automated and manual journal entries, a general ledger, balance sheet, profit and loss statements, and up to five users.

  • Advanced - 79€ (approximately $93) per month for everything in Standard, plus custom fields and up to 10 users with custom roles.

  • Premium - 159€ (approximately $187) per month for everything in Advanced, plus an account manager and up to 25 users.

Before you commit to a plan, you can try Holded’s software free for 14 days (no credit card required).

Best For: Holded is designed for small to mid-sized enterprises, so it works best for growing small businesses or businesses that are currently mid-sized.

5. Best for large enterprises

NetSuite

NetSuite’s Shopify integration offers an impressive level of functionality that makes it a great choice for enterprises. This accounting system is available as a web application and via Android and iOS devices.

Pros

NetSuite allows you to sync real-time customer/order information based on custom triggers and to sync, manage, and centralize inventories, which is especially valuable for larger businesses. It provides in-depth insights into customer purchasing history and buying behavior, automates accounts payable and accounts receivable processes, and ensures domestic and global sales tax compliance via its tax engine.

The integration even includes conditional mapping for data such as currencies, syncing for unlimited orders, order total exports, and more.

While the setup process is relatively simple and user-friendly, NetSuite also offers free setup support via email if you need it. Making sure your account is properly integrated with Shopify from the start will prevent inaccurate orders, customer info, and inventory data.

Cons

While NetSuite is worth its weight in gold for many businesses, it’s a pretty high-powered solution. If you’re on a budget and looking for a Shopify accounting tool that covers the necessary bases but is still cost-effective, you may need to look elsewhere.

Pricing

The base Netsuite license is $999 per month with additional costs for extra users. You can contact the NetSuite team to get an accurate price.

Best For: NetSuite is best for enterprises operating at a large scale and in need of a powerful solution (with customization options) to keep tabs on finances.

6. Best for integration selection

Xero

Xero boasts more than 2 million users, including many Shopify store owners. What sets this accounting solution apart from the pack?

Pros

The Xero App Store features more than 800 integrations. No matter what tools you use to handle your finances and manage your business, chances are that they integrate seamlessly with Xero.

As far as features go, Xero covers all the bases. Its functionalities include transaction reconciliation, automatic sales tax calculation, multi-currency accounting, bill and receipt capture, cash flow and business snapshots, expense claims, and even payroll. Not to mention more than 65 types of financial reports that you can customize and compare in real-time.

And, unlike most accounting apps, Xero allows unlimited users on all of its plans. You can add as many team members as you need to, as well as your bookkeeper, accountant, or tax pro, without the added expense of paying per user per month.

Cons

Some users have reported that Xero isn’t as well-optimized for complex business operations as it is for smaller businesses and that it can be difficult to migrate away from the platform. If your online store takes off and your business grows, it might be a hassle to make Xero work for you or switch to another solution.

Xero also doesn’t offer any options for live customer support over the phone. If you prefer to speak to someone in real-time when you have a question or concern, another solution may be a better fit.

Pricing

Xero has three plans to choose from:

  • Early - $11 per month for the basic plan, which includes up to 20 invoices and quotes, Hubdoc for capturing bills and receipts, bank transaction reconciliation, and short-term cash flow and business snapshots.

  • Growing - $32 per month for everything in Early, plus unlimited invoices, quotes, and bulk transaction reconciliation.

  • Established - $62 per month for everything in Growing, plus support for multiple currencies, project tracking, expense claims, and in-depth analytics.

You can try this tool free for 30 days (no credit card required) to see if it meets your needs.

Best For: Xero can accommodate small, medium, and large businesses, so it’s a great option whether you plan to scale your Shopify business or not.

7. Best hands-off accounting solution

Bench

Sure, the six Shopify accounting solutions listed above are among the best for do-it-yourself bookkeeping and accounting. However, DIY ecommerce accounting isn’t always the best route for a few reasons.

  1. Accounting can be confusing and frustrating, especially when business really starts to take off.

  2. Though DIY accounting software can save you some time, it still requires hands-on management, which takes you away from other important aspects of running your business.

  3. Even the best software is only as accurate as the information you enter into it. If handling the books isn’t your strong suit, even minor errors could throw off your financial reports and negatively impact your business decisions.

That’s where Bench comes in. As with the other solutions mentioned, our software integrates with Shopify and pulls in your financial data to streamline your workflow and generate reports ranging from balance sheets to monthly income statements.

At Bench, though, you don’t have to worry about figuring out accounting software or learning what, exactly, a chart of accounts is. We take monthly bookkeeping and accounting off your hands completely, saving you a ton of time and giving you the peace of mind that comes with knowing that your books are accurate. Don’t worry about data entry or expense categorization—we’re here to help.

We’ve also got major Shopify experience under our belt, with thousands of Shopify store owners that also use Bench for their bookkeeping and accounting. When it comes to producing tax-ready financials for Shopify users, we’ve got you covered.

What's Bench?

We're an online bookkeeping service powered by real humans. Bench gives you a dedicated bookkeeper supported by a team of knowledgeable small business experts. We’re here to take the guesswork out of running your own business—for good. Your bookkeeping team imports bank statements, categorizes transactions, and prepares financial statements every month. Get started with a free month of bookkeeping.


This post is to be used for informational purposes only and does not constitute legal, business, or tax advice. Each person should consult his or her own attorney, business advisor, or tax advisor with respect to matters referenced in this post. Bench assumes no liability for actions taken in reliance upon the information contained herein.

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