6 Best Shopify Accounting Software for 2025

Shopify is a powerful sales channel for small to mid-sized sellers. But it heavily relies on third-party apps for accounting tasks like tax calculations, customs fees, and financial reporting. As a result, you may have to deal with fragmented data across different systems, making it difficult to reconcile expenses and ensure accuracy. 

Even if you spend the median pay of $47,000 to hire a bookkeeper, the challenge remains. Because the disconnected systems still lead to errors and missing numbers. 

Here’s where the best accounting software for Shopify can come in. It will take care of all basic accounting tasks for your store, and a few even automate them to save time and reduce errors. 

Let’s walk through the six best Shopify accounting software to understand why pairing them with an ecommerce integration tool can make your bookkeeping even more efficient. 

6 best Shopify accounting software: A quick overview 

Before we dive into a detailed comparison of Shopify accounting software, here’s a quick rundown of what each one offers.

1. Quickbooks + Webgility

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QuickBooks is the most widely used accounting software for Shopify sellers. 

Unlike basic accounting tools, QuickBooks automates tax calculations, syncs transactions across payment gateways, and ensures compliance with e-commerce tax regulations. Its built-in reporting and reconciliation tools help businesses maintain accurate financial records without constant manual intervention. 

With QuickBooks, Shopify sellers can manage their cash flow and financial health in one centralized platform.

It offers two versions: QuickBooks Online and QuickBooks Desktop. 

QuickBooks Online is a cloud-based accounting solution. It is ideal for businesses seeking easy financial tracking, invoicing, and tax management. 

On the other hand, QuickBooks Desktop is locally installed software on Windows or Mac. It is ideal for businesses needing in-depth accounting and inventory tracking. 

Features

• Automated expense and income tracking:  Syncs bank transactions, categorizes expenses, and tracks profits.
• Custom tags: Tag things as you work to track events, projects, locations, and anything that matters. You can run custom reports based on your tags for an instant view of insights that matter most to you, including expenses, invoices, etc.
• Custom invoicing: Invoicing templates let you create custom, professional invoices, sales receipts and estimates that you can send in minutes, and get paid quicker.
• Tax calculation and compliance: Easily organize expenses into tax categories and track sales tax on income and expenses so you know where you stand and how much you owe.

Why Is QuickBooks + Webgility Integration Better for Shopify Owners?

Users report the following accounting challenges when directly integrating Shopify with QuickBooks:

• Incomplete order data sync – Shopify’s direct connection to QuickBooks lacks detailed order breakdowns, making it difficult to reconcile transactions.
• Payout mismatches – Shopify deposits lump sum payouts into your bank account, which don’t always align with individual transactions in QuickBooks.
• Complicated multi-channel accounting – If you're selling on multiple platforms (Amazon, eBay, or Walmart), QuickBooks alone won’t consolidate financials across all channels.

When they integrate their Shopify store and QuickBooks with Webgility, they can see the following outcomes:

Accurate order and payout reconciliation: Webgility ensures that Shopify payouts are correctly mapped to individual transactions in QuickBooks, eliminating discrepancies and reducing manual corrections.

Multi-channel order syncing:  Webgility syncs sales data from Shopify and multiple sales channels into QuickBooks, keeping your accounting clean and organized.

Automated tax compliance: Instead of manually adjusting tax calculations, Webgility ensures that sales tax is correctly assigned based on Shopify’s tax settings, preventing reporting errors.

Real-time profitability insights: With Webgility’s automation, Shopify sellers can get real-time profit-and-loss reports, track inventory costs, and understand their financial performance at a glance.

Pros

• Users value the wide variety of customizable reports available
• Automates financial tasks, including data entry, reporting, and invoicing
• Easily integrates with third-party apps
• User-friendly interface

Cons 

• If you want near real-time accounting data sync across other sales channels like Amazon, and eBay, you need a third-party integration tool like Webgility
• Doesn’t handle dynamic sales tax rate changes for different states/countries
• Some users report delays in issue resolution

Pricing

Simple: $17/month 

Essentials: $32/month 

Plus: $49/month 

Advanced: $117/month 

All plans include free mobile apps to run your business on the go, QuickBooks support, and app integration.

Ratings 

G2: 4 stars (3,396 reviews) 

2. NetSuite+Webgility

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NetSuite is a cloud ERP suitable for large-scale Shopify businesses with complex financial needs. It’s ideal for enterprise-grade businesses seeking a comprehensive enterprise solution that goes beyond basic accounting.

Shopify sellers using NetSuite gain access to advanced financial reporting, automation, and multi-location tracking. Its automated reporting helps growing e-commerce brands scale without losing financial control. Mid to large-scale Shopify stores with complex inventory, multiple sales channels, or international sales benefit the most from NetSuite’s capabilities.

Features

• Comprehensive accounting and ERP:  Integrates accounting, inventory management, order processing, and customer relationship management (CRM) into a single platform. You can track your business’ financials, inventory, orders, and CRM in one system.
• Multi-channel and multi-currency support: Sync sales from Shopify, Amazon, and eBay. Plus, handles international transactions as it converts currencies automatically and complies with country-specific financial regulations.
• Real-time financial tracking: Provides live updates on cash flow, revenue, and expenses and adapts to multi-state and global tax regulations dynamically.

Why is NetSuite + Webgility integration better for Shopify Sellers?

Directly integrating Shopify with NetSuite creates several challenges for e-commerce businesses:

• Delayed order processing – NetSuite’s native integration with Shopify may not sync orders in real time, causing delays in order fulfillment and inventory updates.
• Manual sales tax adjustments – Shopify’s built-in tax system often doesn’t align perfectly with NetSuite’s tax settings, leading to compliance risks.
• Complex multi-channel management – Selling on multiple platforms (e.g., Amazon, Walmart, eBay) makes it difficult to consolidate financials within NetSuite without additional automation.
• Payout reconciliation issues – Shopify deposits lump sum payouts that don’t always match individual transactions in NetSuite, leading to manual reconciliation headaches.

Benefits of Integrating Webgility with NetSuite

Automated Order and Inventory Syncing: Shopify sellers often face inventory mismatches and order processing delays when relying on manual updates or disconnected systems. Webgility ensures that every new Shopify order is automatically recorded in NetSuite, updating stock levels and payment details in real time.

Multi-Channel Financial Consolidation: Manage sales from Shopify, Amazon, eBay, Walmart, and other platforms in one unified financial system, eliminating duplicate data entry. Sellers get a clear financial picture across all sales channels without spending hours on manual bookkeeping.

Seamless Tax Compliance: Shopify’s built-in tax system may not always align with NetSuite’s tax structure, leading to inconsistent tax reporting across states or countries. Webgility aligns Shopify’s tax calculations with NetSuite’s settings, ensuring tax reporting accuracy across multiple regions.

Effortless Payout Reconciliation: Shopify deposits lump sum payouts into your bank account, making it difficult to match them with individual orders in NetSuite. Webgility maps Shopify payouts to individual transactions—including refunds, discounts, and fees—directly into NetSuite.

Pros 

• All-in-one ERP solution with supply chain, CRM, and HR features
• Integrates with multiple sales channels and POS systems  
• Highly scalable
• Reduces manual data entry by syncing transactions, taxes, and inventory 
• Access data from anywhere 

Cons 

• Expensive for small businesses 
• Complex setup and steep learning curve 
• Not ideal for businesses with simple accounting needs

Pricing

Contact their sales team to get custom pricing. 

Ratings 

G2: 4 stars (3,669 reviews)

3. FreshBooks 

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FreshBooks is ideal accounting software for startups, microbusinesses, and freelancers on Shopify. It comprises all the basic accounting features, from a chart of accounts to bank reconciliation to journal entries. 

Features 

• Remember vendors: All your commonly used vendors will be remembered to make logging your expenses fast and painless.
• Convert estimate to invoice: Once the estimate is approved you can easily transform your custom estimates into ready-to-pay invoices.
• Automated bank reconciliation: Approve, change, and import transactions directly from your bank account.
• Automate late fees: Automatically apply a late fee when your invoice becomes overdue to give your clients that extra incentive to pay you quickly.

Pros

• Comprehensive invoicing features with automation options 
• Responsive customer support
• Intuitive design

Cons 

• Lacks advanced accounting functionalities 
• Higher-tier plans can be costly for startups 
• Some features are less accessible on the mobile app 

Pricing 

Lite: $7.6/month 

Plus: $13.20/month 

Premium: $24/month 

Select: Custom pricing 

Ratings 

G2: 4.5 stars (886 reviews)

4. Xero 

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Xero is a cloud-based accounting platform known for its user-friendly design and powerful integrations. It’s ideal for small Shopify sellers, and businesses based in Australia, the UK, or New Zealand.

Features 

• Automated bank feeds and reconciliation:  Let AI-powered matching reconcile bank statements and automatically connect with your bank to import real-time transactions.
• Multi-currency accounting: Supports 160+ currencies and automates currency conversions for sales, expenses, and invoices.
• Customizable invoicing and payment reminders: Set up automated reminders to chase overdue payments. 

Pros 

• Intuitive interface
• Comprehensive reporting features 
• Easy integration with third-party apps 

Cons 

• Limited functionality for scaling businesses 
• Lacks real-time accounting capabilities
• Some users have experienced difficulties with customer support and responsiveness

Pricing 

Starter: $2.90/month (Usually $29) 

Standard: $4.60/month (Usually $46)

Premium: $6.90/month (Usually $69)

*90% off your plan for 3 months when you buy Xero by 28 February 2025.

Ratings 

G2: 4.3 stars (718 reviews)  

5. Wave

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Wave is a free, cloud-based accounting software for small businesses and solo entrepreneurs. It offers basic financial tools like invoicing, and expense tracking. It also integrates with payment processing and payroll services. 

Features 

• Expense tracking: Monitor your expenses by connecting bank accounts and credit cards for automatic transaction imports. 
  
  
• Receipt scanning: Use the mobile app to capture and store receipts digitally, so you can easily categorize expenses, generate reports, and make tax filing smoother. 
  
  
• Multi-business accounting: Manage accounting across multiple businesses under a single Wave account. 

Pros 

• User-friendly interface that simplifies invoicing and expense tracking 
• Comprehensive financial reporting features despite being free 

Cons 

• Lacks built-in time-tracking capabilities 
• The mobile app doesn’t offer features available in the desktop version
• Some users have reported difficulties in receiving timely assistance

Pricing

Starter: $0

Pro: $16/month 

Ratings 

G2: 4.3 stars (295 reviews) 

6. Sage 

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Sage accounting is a cloud-based solution to assist small and medium-sized businesses in managing their financial operations efficiently. It’s especially appropriate if your business needs robust inventory tracking but can do without mobile access.

Features 

• Customizable invoicing: Create and send professional invoices with customizable templates. 
• Detailed reports:  Get over 150 reports including specialized reports for construction, manufacturing, distribution, and more to make informed business decisions
• Advanced inventory management: Compute and track costs and quantities on a daily basis, based on the transaction date and item class. You can even view quantities on hand, stay on top of purchase orders, and generate reports on valuation and sales. 

Pros 

• Offers a wide range of features including expense tracking, inventory management, and accounting needs 
• In-depth record and transaction forms
• Allows users to access their financial data from anywhere 

Cons 

• Fewer integrations with third-party apps compared to competitors 
• Available only on Windows
• Some UI elements look outdated

Pricing 

Pro accounting: $61.92 

Premium accounting: $103.92/month 

Quantum accounting: $177.17/month 

HR and Payroll bundles: Custom pricing 

Ratings 

G2: 3.9 stars (147 reviews)

Now that you’re familiar with some of the top accounting software for Shopify, let’s dive into how to pick the one that’s right for your business.

How to choose the right Shopify accounting software

Picking the best accounting software largely depends on these three questions:  

Business size: Are you just starting or scaling up? 

Businesses with lean operations benefit most from straightforward, easy-to-use, and cost-effective software. Wave and FreshBooks fit this bill. Wave offers basic accounting features for free, while FreshBooks offers intuitive invoicing and expense tracking, especially for solo entrepreneurs. 

If you’re scaling up and need more robust features, QuickBooks or Xero will support your growing business and help you handle more complex financial needs

Integration needs: Do you sell on multiple platforms?

If you sell on Amazon, eBay, Etsy, or Walmart alongside Shopify or manage multiple payment gateways like PayPal, Stripe, or Square, QuickBooks and Netsuite are your best bets. They sync accounting data across channels, so you don’t have to reconcile financial data manually (which is a nightmare!).

Automation needs: Do you want to eliminate manual bookkeeping?

While NetSuite, Sage, and QuickBooks do offer multi-channel support and some advanced inventory tracking, they fall short when  you want to:

• Sync real-time sales across multiple channels
• Record expenses and handle tax rate changes dynamically across multiple sales channels
• Pull in sales data automatically from all online sales channels 
• Prevent stockouts or overselling with real-time inventory sync across your online marketplaces and POS
• Capture order-specific expenses like shipping, platform fees, or discounts from each channel 
• Automatically consolidate and organize orders across different platforms 

Take Greg Gordon, the founder of PartyMachines, a manufacturer and seller of foam party equipment. He spent two to three weeks every month manually entering numbers into QuickBooks. Hiring an accountant didn’t help much. Managing them took just as much time and required additional payroll and insurance, increasing operational costs.

So how did he consolidate fragmented systems for his growing company? 

Webgility + QuickBooks Online: The best solution for Shopify accounting

Instead of piecing together multiple tools and still struggling with manual work, Webgility + QuickBooks Online is the perfect combination for Shopify sellers who want to automate their accounting.

Once Greg, in the example mentioned above, integrated Webgility, he saved 8–10 hours per day. He previously spent this time on manual data entry. Instead of drowning in spreadsheets, he focused on scaling his business.

Webgiity integrates with QuickBooks Online, QuickBooks Desktop, and NetSuite along with multiple POS systems, stores, and ecommerce marketplaces.  Whether you’re running a brick-and-mortar store alongside your online presence or selling across multiple ecommerce platforms, it captures all your sales and expenses, at both the summary and granular levels, and feeds them into QuickBooks.

You can analyze your margins, marketplace fees, and shipping costs in-depth and get a true picture of your income and expenses by sales channel or payment processor.

Conclusion: Automate ecommerce accounting with Webgility 

Investing in Shopify accounting software without real-time automation will still keep your business in manual mode. If you’re serious about growing your Shopify business without the headache of manual bookkeeping, consider a Shopify accounting software integration tool like Webgility. 

Manual bookkeeping isn’t the only culprit, inventory discrepancies also lead to accounting errors. When these systems don’t reflect the actual amount spent on products sold, it leads to inaccurate financial statements that overstate profits, leading to cash flow problems and chaotic tax filing. 

Webgility solves this by automating the flow of data across your platforms, from syncing inventory to generating accurate financial reports. Get started for free with Webgility and see how much time you can save on manual bookkeeping!