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.
Read on to learn why that's a problem and to explore differences between each tool, including Shopify integrations, COGS tracking, multi-currency support, and everything else you need to know to make a choice.
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.
QuickBooks Online is a comprehensive, integrated solution for ecommerce accounting, if it's paired with the right connectors, and you pick the right plan. It's an especially good choice for merchants selling physical products, stores looking to scale, and robust financial reporting.
QBO connects directly to Shopify and other sales channels, eliminating the need for manual entry of sales, fees, refunds, or payouts. Its tools reduce reconciliation time and produce P&L statements and balance sheets with just a few clicks.
While QBO offers a native Shopify Connector included in your subscription, multi-channel sellers or high-volume sellers may prefer third-party connectors like A2X or MyWorks, which offer more granular payout-level reconciliation and more advanced mapping options.
Expense reporting and a robust dashboard round out QBO's features, but merchants will need to upgrade to at least the Plus plan to benefit from inventory management, COGS tracking, and data on gross margins with no spreadsheets required.
Sales tax compliance support is also limited, with no nexus tracking or automated returns—although a new Beta AI tool does catch discrepancies.
Although $115 per month ends up being the realistic entry point for most ecommerce merchants, QuickBooks routinely offers 50% off deals for the first three months, and there's a free trial before committing. Still, smaller stores may find this price point is too high.
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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.
Xero is a popular cloud-based accounting solution with a modern interface ecommerce merchants often prefer over clunkier platforms offered by legacy software solutions.
It's more affordable than QuickBooks for equivalent core features, and both the Growing and Established tiers are budget-friendly options for ecommerce sellers in need of invoicing, robust reporting tools (65+ reports), and multi-currency support.
Xero especially excels for international cross-border sellers thanks to its support for over 160 currencies, automated exchange rate updates, real-time conversions, built-in compliance tools for GST and VAT, and dedicated foreign currency gain/loss reporting.
But, while its Shopify integration (free to subscribers) syncs sales, refunds, fees, and payouts; matches payments to bank records; and supports flexible tax mapping, it won't apply sales tax rules by location, manage inventory, track COGS, or handle complex multi-channel sales.
Third-party solutions can be layered on top for deeper ecommerce automation. However, U.S.-based sellers with robust inventory management requirements may find that QuickBooks is better at handling these needs.
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.
FreshBooks is a cloud-based accounting and invoicing platform geared for small service-based businesses, freelancers, and agencies. While it excels at creating customized invoices, time tracking, client management, and expense tracking, it lacks key features for ecommerce sellers.
It doesn't offer a native integration with Shopify, doesn't handle inventory management or COGS tracking, and it struggles with high-volume transactions as it's built for client billing, not daily orders. Sales tax support is also limited, as you can track tax but must enter tax rates manually.
Pricing is affordable, and FreshBooks runs frequent promotions to offer even better value. Its $23 tier is a great option if you have a few clients and are just starting operations, as your invoicing software can grow with you. But most ecommerce sellers should look elsewhere.
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.
Zoho Books is a comprehensive cloud-based platform that offers an affordable feature-rich solution for ecommerce sellers. With free plans for small stores and paid plans starting at just $15 per month, Zoho Books is a top choice for cost-conscious merchants.
This software has much more to offer than just a low price, though. It includes core tools Shopify merchants need, including professional invoicing solutions, inventory management, basic COGS calculations in higher-tiered plans, and even expense tracking with receipt scanning.
While Zoho Books doesn't offer the same deep native Shopify integration as some competitors, tools like Zoho Flow and Zoho Inventory (an add-on module) enable real-time inventory management, and improve handling of COGS and fulfillment.
Unfortunately, sales tax compliance is all done manually, as you must set up and maintain different tax rates and rules for different jurisdictions. Zoho Books also doesn't offer automatic nexus tracking or alerts for when you hit the thresholds for required registration with states.
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.
Wave is a free cloud-based accounting and invoicing platform that's popular among new companies without big budgets or high sales volume.
While Wave's starter plan comes at no cost, there are fees for payment processing and the upgraded Pro Plan. This removes Wave Branding from invoices and adds receipt scanning and automatic product categorization and costs $190 per year.
Unfortunately, Wave doesn't offer native Shopify integrations, and using third-party tools to bring in Shopify data is a headache many ecommerce sellers don't want. Wave also lacks meaningful inventory management and automatic COGS tracking, so isn't ideal if you sell physical products.
Wave offers limited support for sales tax, with no economic nexus tracking or autofiling of returns. Wave also doesn't offer automated payout reconciliations or support in handling Shopify fees or managing multiple sales channels.
Most merchants with meaningful sales volume will find the tradeoffs of choosing this free solution simply aren't worth it. But, those who are just getting started and have a low software budget should take a close look at what Wave offers.
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.
Finaloop is a very different solution than every other program on this list because it combines accounting and bookkeeping software with a full human support team. Finaloop is not a DIY tool. A team of professional human accountants handles key tasks and manages your accounting.
If you want a hands-off solution excellent at completing accounting tasks for high-volume or multichannel merchants, Finaloop offers it. Features include automatic COGS and inventory tracking, payout resolution, multi-channel support, and an ecommerce-specific account chart.
Finaloop's prices are higher than software solutions alone, with monthly costs ranging from $245 to $1,900 per month. However, this can still be more cost-effective than hiring an accounting team. That's especially true given that Finaloop handles sales tax compliance too.
Finaloop also offers native integration with Shopify, multi-channel support, and real-time reporting with up-to-date P&L statements, balance sheets, cash-flow statements, and founder-friendly dashboards tailored to the most important ecommerce KPIs.
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.
A2X is not traditional accounting software. Instead, it fills a gap many accounting platforms create. Specifically, the integration between accounting tools and Shopify (or other sales channels) sometimes leaves merchants coping with messy settlement matching.
If your accounting software imports a lump sum Shopify payment including sales, refunds, fees, and shipping, you'll need to manually reconcile each component—a time-consuming task that introduces potential for human error.
A2X solves this problem, transforming high-volume payout data from sales channels into clean, accurate invoices or journal entries that can be properly categorized and used to ensure your bank deposits match up with expected payments.
When A2X breaks down your transactions, it shows sales revenue; refunds; fees; shipping costs; gift cards; discounts, and collected sales, VAT, or GST.
It handles multi-currency stores, supports online and in-person Shopify sales, and its Shopify Cost Sync feature even pulls SKUs directly from Shopify to create accurate COGS entries.
To use A2X, you must connect it to your Shopify store and other sales channels, then connect it to your accounting software. It will run automatically in the background, providing your accounting software with the information it needs to work for you.
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.
Usually, this means ensuring you're transferring data seamlessly, that the data is accurate, and that your tools perform the necessary tasks. To achieve these key objectives, features that you should look for in accounting software that works with Shopify include the following.
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.
Native Shopify integrations, like those with QuickBooks and Xero, make setup easier and data transfer more seamlessly while other tools require middleware like A2X.
What most merchants should avoid, though, is programs relying on CSV imports or manual data transfers, all of which introduce the potential for human error and take up company time.
2) Sales data accuracy
Shopify sends accounting programs lump-sum payout data that include sales, refunds, fees, and shipping—not individual transactions.
If your accounting tool can't break out these transactions into their individual components, you could end up with reconciliation nightmares, inaccurate revenue and gross margin data, and profit-and-loss statements that don't reflect reality.
The right accounting tools will automatically summarize and categorize each payout, post clean invoices or journal entries that reconcile with your bank deposits, and handle complexities like multi-currency sales or late refunds effectively.
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.
Not every accounting tool excels at COGS tracking, or even offers it, especially free or low-cost tools. Look for programs that provide real-time or automated calculation, automatic inventory quality and cost tracking that adjust with sales, and support for FIFO and landed costs.
4) Sales tax features
Sales tax compliance is critical to avoid audits and penalties. Most accounting software does little to help. Invoicing tools may include sales tax (calculated automatically or manually) and accounting tools record sales tax collections but that's usually the extent of the support.
Far too many Shopify merchants don't realize this leads to major compliance gaps, as the software doesn't monitor nexus thresholds, register your company in new states when required, file sales tax returns or help you remit payment. These tasks must be managed separately.
That said, the best accounting software offer at least some support in this category, such as helping with tax rate calculations.
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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. There are also free solutions with less robust features or paid options that require you to choose a tier based on transaction volume or other factors.
The focus should be on finding a tool that provides the best value, balancing the data importing and reporting features with monthly fees. It's also a good idea to find a solution that grows with your company as changing accounting tools can be burdensome.
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.
Most states in the U.S. require sellers to collect and remit sales tax from in-state customers if the seller has physical or economic nexus within the state. Physical nexus means having a local presence. Economic nexus means surpassing the state's threshold for revenue or transactions.
Shopify stores selling at the national level at a meaningful volume might have nexus in 10, 20, 30, or more states, each of which has its own sales tax rates, rules for what's taxable, and sales tax filing schedule. Failing to comply with any rules in any state creates audit risks.
Accounting software typically doesn't tell you when you must collect sales tax or at what rate. It won't track nexus or alert you when you must register, nor will it collect the correct sales tax from clients, autofile sales tax forms, or send payments on schedule.
And Shopify can collect sales tax for sellers if you set it up properly, but it doesn’t handle filing/remitting.
Manually tracking and managing sales tax compliance tasks is difficult or impossible, especially as accounting software usually just summarizes transactions by state without offering details on which items were taxable or at what rates.
Another solution is essential. And using a Shopify sales tax app, like Numeral, is that best solution.
Numeral was built for sales tax compliance and offers free nexus monitoring, autoregistration with states, filing/remitting, and expert review before each return is submitted.
Numeral backs its work with the Numeral Guarantee, covering fees, penalties, and filing costs if we miss a filing or make an error that results in post-audit penalties. It works with your accounting software and complements it, ensuring you follow all state tax laws.
And, the price is affordable: nexus monitoring is free, there are no commitments, and the standard plan charges just $75 per filing and $150 per registration.
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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.
However, both are limited in their features, and stores with higher order volumes may prefer more robust solutions like QuickBooks Online or Xero.
Does Shopify have built-in accounting?
Shopify provides some basic financial reports, but isn't a full-featured accounting solution. Shopify doesn't provide bank reconciliation, COGS calculation, sales tax filing, or robust reporting tools.
Most merchants use a dedicated tool that integrates with Shopify to fulfill accounting or bookkeeping tasks. Merchants selling across multiple states also need software to help with sales tax compliance, which most accounting tools don't manage.
Do I need accounting software if I use Shopify Payments?
Shopify Payments processes payments but doesn't handle bookkeeping on your behalf. Shopify Payment Deposits are also lump sum payments, so each transaction must be reconciled and recorded properly. 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.
Numeral handles these tasks and works in conjunction with your accounting software. Numeral also integrates with Shopify and other ecommerce platforms.
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.
The right choice will depend on your budget, geography, and whether you sell in multiple currencies.
What is A2X, and do I need it?
A2X is a reconciliation connector that helps your accounting software work better with Shopify. While Shopify usually reports payments to accounting software as lump sums and not mapped to individual transactions, A2X ensures data is broken down to make reconciliation simple.
Multi-channel or high volume sellers can use A2X to break down transactions into revenue, sales, refunds, fees, shipping, discounts, and more. This is especially beneficial for high volume sellers and multi-channel sellers using tools like QBO and Xero for accounting.
