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Best accounting software for Shopify: 5 excellent options to consider

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Shopify has gained a reputation as an ecommerce powerhouse, with over one million businesses using its site builder and point-of-sale services. With its affordable platform and robust business management tools, it’s no surprise many merchants get started with Shopify.

But even the best business software can’t do it all. Accounting software fills in the gaps, letting you track income and expenses, run reports, prepare for tax time, send and receive payments, and more. 

Hopefully, you’ve already registered your business, opened a business bank account, and have your business records in order, so you’re ready to sign up for accounting software. (If not, check out our quick guide to small business accounting and bookkeeping.) 

Now, it’s time to go comparison-shopping. Here are five top options offering the best accounting software for Shopify.

Best accounting software for Shopify store owners

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All of the accounting software options we’ve compiled are cloud-based, which means you can access your data anytime, anywhere, from any device connected to the internet. Cloud solutions help you avoid manual data entry mistakes that are easy to make when you’re copying over sales figures and other information.

One important note: Most accounting software doesn’t directly integrate with Shopify. You may have to find an app connector in the Shopify App Store, or use apps like Zapier and A2X to set up the integration. Most apps include easy-to-follow instructions, so you can manage setup without calling a software developer. 

FreshBooks

FreshBooks is solid accounting software for small business owners on Shopify, freelancers, and microbusinesses. The platform covers all the basics, from a chart of accounts and bank reconciliation to items and journal entries. 

FreshBooks supports more than 170 different currencies, making it a convenient solution for international ecommerce businesses. If you offer services, you get access to unlimited invoices, estimates, time tracking, and mileage tracking. There’s also a FreshBooks mobile app for iOS and Android.

Compared to other accounting tools, FreshBooks has a few uncommon restrictions. Each plan includes only one user, and it costs to add more. You can invite users to view certain sections, and set permissions on an individual basis. 

Double-entry accounting isn’t available on the starter plan. Customers often request a more expansive array of reports, invoice templates, and available currencies. That said, Freshbooks remains a popular small business accounting app. 

Cost: Freshbooks starts at $15 per month for the Lite plan. 

NetSuite

Another way to streamline your back office is to integrate NetSuite with your Shopify online store. NetSuite is an enterprise resource planning (ERP) system that lets you oversee most of your options without any hassle. Automate key areas like financial management, and optimize even further with NetSuite's order, billing, customer, and inventory management features.

NetSuite offers custom accounting tools at the enterprise level. Improve control over your accounts receivable and accounts payable, as well as fixed asset management. You can also rest easy knowing NetSuite’s tax engine handles your domestic and global sales tax compliance

As an all-in-one accounting system, NetSuite’s pricing is on the high end compared to other options. But for a scalable solution that seamlessly handles your financial data and sales channels, NetSuite is a strong contender.

Cost: Contact NetSuite for a package quote tailored to your business. 

Brex customers: Simplify your payments and financials even further with the Brex + NetSuite integration.

QuickBooks Online 

QuickBooks is likely the most familiar name in business accounting software, and for good reason. It’s a Shopify-ready solution designed for small and mid-sized businesses across various industry verticals and business needs. 

Of all the options on this list, QuickBooks has some of the most impressive features. You can easily keep track of your invoicing, bank account balances, cost of goods sold, profits and losses, cash flow, vendor bills, and more. Tap into receipt capture features, and hundreds of integrations with platforms like Amazon, PayPal, and Square. 

Each of the four plans gives you access to an intuitive mobile app for Apple and Android devices, as well as real-time reporting features. More advanced plans open up project management tools and let you track inventory and time. All this makes QuickBooks one of the best accounting software options for Shopify users.

Cost: QuickBooks Online starts at $12.50 per month for the Simple Start plan.

Brex customers: Save time and improve accounting accuracy with our Brex + QuickBooks integration.

Wave 

Manage your sales, purchases, accounting, banking, and reports end to end with Wave, a free accounting software. Unlike some free software options, there’s no fine print to parse. Wave offers a simple, no-cost accounting platform you can connect to your Shopify store. 

Wave’s target market is small business owners and freelancers who mostly accept credit card payments. It’s easy to use even if you have no financial management experience and offers a lot of functionality for a free tool. 

Simply connect your bank account to Wave, integrate Wave with Spotify, and watch transactions flow between each platform. Stay on top of your expense management by uploading receipts directly to Wave with the snap of a picture. 

There are some drawbacks to this free software. There’s no comprehensive mobile app, just a Wave invoicing and receipt scanning app. If you work with a bookkeeper, accountant, or tax professional, you’ll likely need more robust software. Wave lacks the reporting features and customization needed for a growing business. 

Cost: Accounting by Wave is free to use. 

Xero

As an ecommerce business owner, you aren’t tied to any one store or location. Xero, the final Shopify accounting solution on our list, has a similar mindset. Xero’s platform includes ample features, customizable financial reports, and over 800 integrations for small, medium, and large businesses. You can manage it all from your smartphone or tablet thanks to its high-quality mobile app. 

Notably, Xero supports unlimited users on every plan, which isn’t common in the accounting universe. Add your team members, bookkeeper, accountant, or tax professional as needed. From there, you can take care of payments, accounts, and inventory with confidence.

However, you need to upgrade plans to get unlimited bank transactions. The same goes for adding multiple currencies, expense claims, and project time tracking to your ecommerce platform. 

Customers praise Xero’s user-friendly layout. By contrast, not every Xero user will prefer their customer support options. There is no live phone support, although you can reach out via email, live chat, and your Xero account. If you’re focused on features and integrations, Xero offers everything you need in a cloud accounting system. 

Cost: Xero’s accounting software starts at $9 per month for the Early plan.

Brex customers: Leave Excel sheets and time-consuming data entry behind with our Brex + Xero integration

Simplify your Shopify store

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Now that we’ve covered the best accounting software for Shopify stores, you’ve seen how simple it is to sync up your systems and improve efficiency across the board. 

If you still have questions about how to choose the right accounting software, check out our podcast on accounting for startups. We cover when to sign up, who should have access to your platform, and what sets the most popular accounting software options apart.

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