Best Shopify Accounting Software: Comparing Prices & Features

Accounting software solutions are plentiful, but most weren't built for ecommerce. This guide helps Shopify stores find tools that actually work by detailing integrations, cost, and features. It also shows how accounting/bookkeeping software falls short, creating a risky tax gap.

By Christy Bieber
Content Creator
Christy is a personal finance and legal writer with a JD from University of California, Los Angeles. She has written for WSJ Buy Side, Fox Business, CBS MoneyWatch, Miami Herald, CNN Underscored, and more.

Reviewed by Nate Matherson
Head of Growth
Nate is the Head of Growth at Numeral. He has founded multiple venture-backed companies and is a two-time Y Combinator Alum. He is based in Charleston, SC.

Published: May 14, 2026

Shopify makes selling easy, but it doesn't help with many critical tasks after a sale.

Good accounting software tracks expenses and the cost of goods sold, prepares financial statements, and handles reconciliation. Unfortunately, many Shopify sellers don't have the right software.

Tools like QuickBooks and Xero are widely used, partly because many sellers pick software on name recognition alone. Unfortunately, legacy solutions aren't always a good fit for ecommerce, leaving sellers vulnerable to messy books, reconciliation headaches, and sales tax blind spots.

The best accounting software for Shopify sellers depends on things like size, location, priorities, and how hands-on you want to be. For example, Wave and Zoho Books are ideal for cost-conscious sellers, while Finaloop and A2X shine for ecommerce-native automation.

This guide showcases seven tools, all of which excel at the basics, like P&L statements, bank reconciliation, and financial reporting.

7 Best Shopify Accounting Software Options

There's no single best accounting software for every company. The right choice depends on your budget, goals, required integrations, and more.

Our comparison table shows the basics of popular accounting tools to offer insight into what may work for you:

1) QuickBooks Online

QuickBooks Online is the most widely used accounting platform in the US, and it has the strongest Shopify-compatible integrations of any tool on this list.

• Best for: US-based Shopify merchants in need of full-featured accounting, robust reporting, payroll integration, inventory tracking, and a wide app ecosystem.
• Who should skip: Merchants outside the US who require better multi-currency support, or early-stage stores where the monthly cost is hard to justify.
• Starting price: $38 month for Simple Start. Most users need Plus ($115) or Advanced ($275).
• Shopify integration: Free native QuickBooks Connector in the Shopify App Store; third-party options like MyWorks or A2X offer deeper syncing for high-volume stores.
• Sales tax features: Calculates and records sales tax by jurisdiction; does not monitor nexus thresholds or file returns. Beta AI program helps identify discrepancies.
• Free plan: No. A 30-day free trial is available.

2) Xero

Xero is a cloud-based accounting platform with a strong following in the UK, Australia, and New Zealand. It's also an option for US-based Shopify merchants who sell internationally or need built-in multi-currency accounting.

• Best for: International merchants, UK/AU/NZ-based Shopify stores, and US merchants with robust multi-currency accounting needs.
• Who should skip: US-based merchants with purely domestic sales or who are looking for cheaper solutions.
• Starting price: $25 month (Early plan which offers limited invoices/bills); most merchants need Growing ($55) or Established ($90).
• Shopify integration: Free native integration available in the Shopify App Store; syncs sales data, payouts, and refunds.
• Sales tax features: Supports VAT, GST, and US sales tax tracking; doesn't auto-file returns or manage nexus.
• Free plan: No. 30-day free trial available.

3) FreshBooks

FreshBooks is designed primarily for freelancers and service businesses, not ecommerce stores. It appears on most "best Shopify accounting software" lists because it's popular and affordable, but its fit for Shopify merchants is narrow.

• Best for: Freelancers or service providers who also run a small Shopify store and need strong invoicing and time tracking.
• Who should skip: If you're a higher volume seller, sell physical goods, or want native integration with Shopify tools, FreshBooks isn't a fit.
• Starting price: $23/month for lite plan (Invoice up to 5 clients); up to $70/month if you have contractors or need to invoice an unlimited number of clients.
• Shopify integration: No native integration; requires Zapier or a third-party connector, which is less seamless than QBO or Xero.
• Sales tax features: Minimal; not designed for multi-state ecommerce sales tax compliance.
• Free plan: No; 30-day free trial available.

4) Zoho Books

Zoho Books is an underrated option that offers a surprisingly full set of accounting features at a fraction of the cost of QuickBooks or Xero. It also includes a genuinely useful free plan for businesses with under $50,000 in annual revenue.

• Best for: Budget-conscious merchants who want solid ecommerce accounting without the higher monthly price tag of QBO or Xero.
• Who should skip: High-volume sellers who need native payout syncing and advanced ecommerce reconciliation tools may prefer either QuickBooks or Xero, both of which have better native integrations and third-party connectors with Shopify.
• Starting price: Free (for businesses under $50k annual revenue); paid plans from $15/month.
• Shopify integration: Integrate using tools like Zoho Flow, third-party connectors, or Zoho Inventory (an add-on module in the Zoho ecosystem).
• Sales tax features: Supports US sales tax, GST, and VAT; basic calculation and recording; no auto-filing.
• Free plan: Yes, with a $50,000 annual revenue cap.

5) Wave

Wave is a free accounting platform that covers the essentials: Invoicing, expense tracking, bank reconciliation, and basic reporting. For very small or just-launched Shopify stores, it can handle the basics at zero cost.

• Best for: Early-stage Shopify stores and solopreneurs who need basic bookkeeping and aren't yet ready to pay for full accounting software.
• Who should skip: Any merchant with meaningful sales volume, multi-channel or cross-border sales, or a need to track inventory value and COGS.
• Starting price: Free starter plan for accounting module only; payments processing and payroll are paid add-ons.
• Shopify integration: No native integration; requires a third-party connector (Zapier or similar).
• Sales tax features: Minimal; not designed for multi-state ecommerce compliance.
• Free plan: Yes.

6) Finaloop

Finaloop isn't typical accounting software. It's built to solve the problems general account software can't handle. Its ecommerce-native accounting service combines automated bookkeeping with a team of human accountants specializing in DTC brands.

• Best for: Growing Shopify-first DTC brands who want accurate, ecommerce-specific books without doing the accounting themselves.
• Who should skip? Price-conscious merchants who would rather manage a DIY setup using tools like Quickbooks than pay the added price for professional bookkeeping and accounting support.
• Starting price: $245-$1,900/month.
• Shopify integration: Deep native integration; syncs orders, returns, COGS, payouts, and data from other sales channels.
• Sales tax features: Sales tax tracking is included as part of the service.
• Free plan: No.

7) A2X

A2X isn't a traditional accounting platform. It's a reconciliation connector that sits between Shopify and accounting software like QuickBooks or Xero. It solves a painful problem resulting from Shopify integrations with limited data transfer capabilities that make reconciliation difficult.

• Best for: Shopify merchants who already use QuickBooks Online or Xero and need accurate, automated reconciliation of Shopify payouts.
• Who should skip? Low-volume merchants who can manage manual entry efficiently and merchants using Finaloop (which manages Shopify data for you seamlessly as part of its service).
• Starting price: ~$29-$115/month for a single ecommerce platform; $89-$229/month for multichannel sellers.
• Shopify integration: Works alongside QuickBooks or Xero; maps Shopify payouts to individual transactions automatically.
• Sales tax features: Maps sales tax collected to individual transactions; does not file returns or track nexus.
• Free plan: No; free trial available.

What to look for in Shopify accounting software

With so many Shopify accounting software options, finding the right one requires you to understand what features most impact your user experience.

1) Shopify integration quality

Accounting tools are only as good as the data provided.

Your tool's Shopify connection must sync automatically, in near-real time, and provide detailed information for reconciliation.

2) Sales data accuracy

Shopify sends accounting programs lump-sum payout data that include sales, refunds, fees, and shipping—not individual transactions.

3) COGS and inventory tracking

If you carry physical products, you can't just track revenue. You must accurately track the cost of goods sold in order to assign the right value to your inventory, and correctly calculate gross profit margins.

4) Sales tax features

Sales tax compliance is critical to avoid audits and penalties. Most accounting software does little to help.

5) Pricing vs. order volume

Pricing matters, especially for startups with tight budgets. Some tools charge flat monthly fees while others scale with order volume.

What accounting software won't do: The sales tax gap

All the tools in this guide can handle bookkeeping effectively for the right users. Unfortunately, accounting software has a major gap: It does not handle sales tax compliance.

Shopify accounting software FAQs

What's the best free accounting software for Shopify?

The best accounting software for Shopify depends on your needs. Wave is a widely used free option, while Zoho Books also offers a free plan if your revenue is under $50,000.

Does Shopify have built-in accounting?

Shopify provides some basic financial reports, but isn't a full-featured ecommerce accounting solution. Most merchants use a dedicated tool that integrates with Shopify to fulfill accounting or bookkeeping tasks.

Do I need accounting software if I use Shopify Payments?

Shopify Payments processes payments but doesn't handle bookkeeping on your behalf. Accounting software tackles these tasks and integrates with Shopify.

Does accounting software handle Shopify sales tax?

Accounting software can record tax collected on Shopify sales but generally doesn't provide full compliance solutions. You'll need another tool to monitor for nexus, register you in states when required, and file and remit tax payments.

Is QuickBooks or Xero better for Shopify?

QBO can be a better option for U.S. based merchants because it offers stronger integrations and more comprehensive ecommerce features. Xero is best for UK, AU, NZ, and international sellers and may also come at a lower cost than QuickBooks online.

What is A2X, and do I need it?

A2X is a reconciliation connector that helps your accounting software work better with Shopify. It ensures data is broken down to make reconciliation simple.