The Best Ecommerce Accounting Software in 2025

The rise of AI technology now helps streamline your ecommerce accounting tasks and save valuable time.

“From an accounting perspective, I think bookkeeping is actually getting easier for small businesses,” says Marc Van den Dobbelsteen, Shopify’s director of accounting. “A lot of the systems that are being developed now have some AI capabilities or some automation built into them, which saves you a lot of time on the back end.”

Ahead, we’ve rounded up nine top accounting software platforms to help you find the best accounting solution for your ecommerce business.

9 best ecommerce accounting software solutions

1. QuickBooks Online
2. Wave
3. Zoho Books
4. FreshBooks
5. Sage 50 Accounting
6. Xero
7. GnuCash
8. NetSuite
9. Striven

Platform	Monthly starting price	G2 ⭐️ rating	Best for
QuickBooks Online	$38	4.0	Comprehensive software
Wave	Free	4.3	Free plan
Zoho Books	$20	4.5	Working with an accountant
FreshBooks	$21	4.5	Hourly contractors
Sage 50 Accounting	$61.92	4.5	Complex accounting
Xero	$20	4.3	Hands-on support
GnuCash	Free	4.2	Tech-savvy business owners
NetSuite	Price upon request	4.1	Enterprises
Striven	$35	4.5	Larger small businesses

Whether you’re just starting out as a solopreneur or managing a growing online company, the ideal accounting software for your small business is out there. Take a look at these nine options to help you with your ecommerce accounting:

1. QuickBooks Online

You may have already heard of the accounting software QuickBooks. This well-established double entry accounting software is used by more than 1.4 million businesses.

Today, QuickBooks comes in a cloud-based version called QuickBooks Online, featuring AI capabilities. (QuickBooks discontinued its standard desktop product in May 2025, leaving QuickBooks Enterprise as the only desktop option.) AI tools in QuickBooks Online include invoice generation, payment recommendations, and automated expense reports—you can send a photo or email of an expense, and the system records it automatically.

QuickBooks’s cloud-based accounting software offers a straightforward interface with essential tools like cash flow tracking and bookkeeping automation. It also connects more than 800 apps, from time tracking and payroll tools to marketplace connectors.

To access services like multi-currency transactions or attaching billable hours to projects, you’ll need a higher-tier plan. Inventory tools are limited to the Plus and Advanced packages. QuickBooks also sells an Enterprise version ($2,210–$5,364 per year) with advanced payroll and reporting features.

QuickBooks integrates with hundreds of third-party apps, including Shopify. By installing the Shopify Connector app, you can automatically import orders and payouts from your online store into QuickBooks.

Who it’s for

Small businesses looking for a feature-rich accounting solution.

Pricing

• Simple Start: $38 per month for automated bookkeeping, basic reports, auto-calculated sales tax.
• Essentials: $75 per month to facilitate multiple-currency transactions, connect three sales channels, and provide detailed reports.
• Plus: $115 per month for additional features like profit projections, financial plan generation, and inventory management and tracking.
• Advanced: $275 per month for tools geared toward larger companies, including 25-user collaboration, automated workflows, and unlimited custom reports.

Features

• AI-powered expense organization
• Free Shopify integration
• Mobile app
• Auto-generated invoices and expense reports
• AI-powered receipt scanning
• G2 ⭐️ rating: 4

2. Wave

Wave offers a free version of its accounting software for businesses with simple accounting needs. The free starter plan includes the basic features needed to manage your small business’s finances: unlimited invoices and records, online payments, and professional invoices.

Upgrading to Wave’s paid plan removes Wave branding and unlocks automation features like auto-imported bank transactions and automatic categorization. Wave connects to Shopify via Zapier.

Who it’s for

Freelancers looking for a free plan.

Pricing

• Starter: $0 per month for unlimited estimates, invoices, and bookkeeping records.
• Pro: $16 per month for automated bank transactions import, late payment reminders, receipt capture, and more.

Features

• Expense organization
• Shopify integration via Zapier
• Mobile app
• Auto-generated invoices
• Receipt scanning with additional subscription
• G2 ⭐️ rating: 4.3

3. Zoho Books

Zoho Books offers a free version of its online accounting software to companies earning less than $50,000 annually—an attractive option for small ecommerce businesses on tight budgets. The free plan also supports 1099 contractors and lets you share access with an accountant.

The platform offers essential accounting features like invoice generation and expense tracking with built-in categorization. Zoho Books includes inventory tracking features through its Zoho Inventory tool, available with an added subscription. 

Zoho Books offers a Shopify integration through its product Flow (starting at $25 per month) and the Zia AI assistant tool, which automates tasks like document and spreadsheet management.

Who it’s for

Small businesses working with an accountant.

Pricing

• Free: Basic bookkeeping and accounting tools for businesses with less than $50,000 in annual revenue.
• Standard: $20 per month for everything in Free, plus additional tools including custom financial reports and fields, bank feed connection, and sales tax tracking.
• Professional: $50 per month for more features like multi-currency transactions, timesheet billing, and inventory tracking.
• Premium: $70 per month for advanced accounting tools, including budget management, cash flow forecasting, and the ability to design custom accounting functions.

Features

• Shopify integration with an additional subscription
• Mobile app
• Auto-generated invoices and expense reports
• Inventory management with an additional subscription
• Receipt scanning
• G2 ⭐️ rating: 4.5

4. FreshBooks

FreshBooks is an accounting software known for its ease of use, with more than 30 million businesses relying on it. Features like retainers and hour tracking make it a good option for independent contractors.

The lowest-priced plan covers invoicing and basic accounting, like expense and income tracking, but comes with notable limitations: only five billable clients and extra fees for collaborators.

The program’s more expensive plans add automation, including scheduled emails (like payment reminders and confirmations) and profit projections. However, the software does not offer AI tools. 

Connecting Freshbooks with Shopify requires a third-party app like Zapier, which automates importing your Shopify data into Freshbooks.

Who it’s for

Best for hourly contractors.

Pricing

• Lite: $21 per month for unlimited invoices to five clients and basic services like expense tracking.
• Plus: $38 per month for unlimited invoices to 50 clients and automations like receipt capture.
• Premium: $65 per month for unlimited invoices to unlimited clients and increased customization and automation capability.

Features

• Shopify integration via Zapier
• Mobile app
• Auto-generated invoices and expense reports
• Inventory management
• Receipt scanning
• G2 ⭐️ rating: 4.5

5. Sage 50 Accounting

Sage 50 Accounting is pricier than many competitors but includes advanced features. These range from financial forecasting for what-if scenarios to job costing tools that compare project expenses against revenue.

The software also integrates with Sage 50’s human resources platform to manage payroll deductions and other labor costs, making it a good fit for small businesses with growing HR needs. Plus, Sage 50’s AI helps catch errors, automate end-of-month closings, and send invoices.

Shopify integration requires a third-party app like Zapier.

Who it’s for

Companies with more complex accounting needs.

Pricing

• Pro: $61.92 per month for one user and features including automated bank reconciliation, invoice and bill tracking, and job costing.
• Premium: $109.67 per month for up to 5 users, industry-specific functionality, and multicompany integration.
• Quantum: $188.67 per month for up to 40 users, workflow management, and role-based user permissions.

Features

• AI tools
• Auto-import bank transactions
• Mobile app
• Auto-generated invoices and expense reports
• Mobile app
• Inventory management
• Receipt scanning with additional subscription
• G2 ⭐️ rating: 3.9

6. Xero

Xero is an accounting software built for small businesses and solopreneurs. The platform offers free access to onboarding specialists during the first 90 days, easing the learning curve for accounting newbies.

Beyond accounting essentials, Xero offers a digital assistant powered by generative AI. Its assistant, JAX, handles tasks like generating invoices and editing quotes.

Xero integrates with Shopify via a free app (for merchants in the US and Canada; $13 per month elsewhere). The app syncs orders, payouts, and sales tax between Xero and Shopify.

Who it’s for

Small business owners looking for hands-on support.

Pricing

• Early: $20 per month for five bills, 20 invoices, and basic features like bank transaction reconciliation.
• Growing: $47 per month for unlimited bills and invoices, plus bulk reconciliation.
• Established: $80 per month for additional features, including multicurrency transactions, project tracking, and expense claiming.

Features

• AI tools
• Free Shopify integration
• Mobile app
• Auto-generated invoices
• Inventory management
• Receipt scanning
• G2 ⭐️ rating: 4.3

Read more: The Entrepreneur’s Guide to Small Business Finance and Accounting

7. GnuCash

GnuCash is a completely free open-source accounting software. It’s a desktop product, so you’ll need to download it to your computer, and it can’t be accessed remotely.

If you’re tech-savvy, you can customize GnuCash’s code to fit your needs. However, its interface feels dated, it lacks automation and AI tools, and it doesn’t integrate with Shopify.

Who it’s for

Tech-savvy business owners who want to customize their accounting software.

Pricing

• GnuCash is completely free.

Features

• Open-source
• Downloadable desktop software
• Advanced customization with coding
• G2 ⭐️ rating: 4.2

8. NetSuite

NetSuite Cloud Accounting by Oracle is an enterprise-level software that integrates with Oracle’s other NetSuite products. These include customer management, inventory and order management, and HR, making it a good choice for large businesses that want a unified tech stack.

NetSuite Cloud Accounting offers advanced reporting tools to help big companies analyze cash flow. It also tracks depreciating and appreciating assets, manages local taxes across subsidiaries, and provides other enterprise-grade features.

Automations help accelerate tasks like account reconciliations, and AI tools scan invoices, flag anomalies, and more. A paid Shopify App ($199.92 per month) syncs inventory, pricing, product, sales, and fulfillment data between NetSuite and your Shopify storefront.

Who it’s for

Enterprises looking for a unified tech stack.

Pricing

• Price upon request.

Features

• AI-powered expense organization
• Advanced reporting
• Paid Shopify integration
• Mobile app
• Auto-generated invoices and expense reports
• G2 ⭐️ rating: 4.1

9. Striven

Striven is a broad business platform with tools for HR, customer relationship management (CRM), and more—including cloud accounting that covers the essentials for managing your small business’s finances.

Striven Cloud Accounting has tools to support tax compliance, integrate with payroll, and generate detailed reports. Automations assist with invoicing, while AI helps with cash forecasting, receipt tracking, and more.

You can integrate Striven with your Shopify storefront through a third-party app like Zapier. Striven also offers industry-specific solutions, tailoring its products for industries like supply chain, construction, and ecommerce.

Note that Striven’s pricing is per-user, so costs can climb quickly if multiple users need access.

Best for

Larger small businesses with a small number of accountants.

Pricing

• Standard: $35 per month per user for up to 100,000 inventory items, 1,000 inventory locations, financial reports, bank reconciliations, and more.
• Enterprise: $70 per month per user for up to 500,000 inventory items, unlimited inventory locations, and more.

Features

• AI tools
• Shopify integration via Zapier
• Mobile app
• Auto-generated invoices
• Inventory management
• Receipt scanning
• G2 ⭐️ rating: 4.5 for general Striven software

Factors to consider when choosing the best accounting software for your ecommerce business

• AI tools
• Scanning receipts
• Scalability and number of supported users
• Cloud-based vs. desktop
• Support
• Automations and invoicing
• Shopify integrations
• Extra features

There’s a lot to consider when choosing the best accounting software for your ecommerce business. Are you looking for a simple tool to automate bookkeeping tasks like logging receipts? Or do you need a more comprehensive platform that generates performance reports, manages inventory, produces profit and loss statements, and helps you with cash flow management?

The following considerations will help you hone in on the right small business accounting software for your business. Before you get started, set yourself up for success by taking essential small business accounting steps like opening a business bank account and establishing a process for collecting sales tax.

AI tools

Most of the best accounting software now includes AI. These tools can do everything from generating invoices and expense reports to managing documents—and in some cases, catching errors—saving you valuable time.

Scanning receipts

Logging expense receipts is essential but time-consuming. Luckily, many accounting platforms now offer receipt-scanning technology to help.

“You can take a picture of the receipt, [the software] can read the receipt for you, and it can categorize it for you automatically—versus having to do that all manually before,” says Shopify’s director of accounting, Marc Dobbelsteen. “It saves a lot of time in the back end.”

If you run a business with many expenses to log, look for software that offers this technology.

Scalability and number of supported users

If you plan to grow your business, you might eventually require more complex accounting tools like job costing or advanced financial forecasting. Think about how much and how quickly you intend to grow, and consider whether your chosen software offers higher-tier subscriptions that can facilitate your growth. Otherwise, you may need to switch platforms later—an expensive and time-consuming transition.

You’ll also want to consider the number of supported users. Many accounting platforms restrict users on lower-tier plans. This might not be a problem if you’re a solopreneur, but if you plan to grow and bring in employees or accountants, factor in the cost of adding users when comparing plans.

Cloud-based vs. desktop

Today, almost all accounting platforms for small businesses are cloud-based. That means your data lives on the internet rather than on your computer. Benefits include access on the go, shared access for team members, and easy integration with tools like Shopify. You’ll pay a monthly or yearly subscription for these cloud accounting platforms.

Desktop accounting software, on the other hand, might pose lower security risks, and may cost less in the long run, since you buy the software upfront and pay only for periodic updates rather than recurring subscription fees.

Support

There might be times when you need help with your accounting software, especially in the beginning. Consider looking for a platform with phone support rather than chat-only support. Higher-tier plans may also offer more specialized help.

Automations and invoicing

How many different types of expenses and payments do you have each month? If you’re processing a large number of financial transactions, automations like autocategorized receipts and auto-generated expense reports can help you speed up the accounting process.

These automations can also benefit your invoicing process: Sending invoices can be a repetitive task prone to small errors, but many platforms automate the process of writing and sending invoices. If you create and send a lot of invoices (for example, maybe you’re a freelancer or a wholesale retailer), choose software that can handle this automatically.

Shopify integrations

A seamless integration with ecommerce accounting software eliminates the need for manual data entry. If you’re a Shopify merchant, you can connect your store directly with accounting platforms like QuickBooks, Zoho Books, or Xero.

These integrations reduce the risk of errors from manual entry by importing data directly from your store.

Extra features

Some accounting platforms offer functionality to help with non-accounting aspects of your business, like human resources and inventory management. Before choosing a platform, consider which extras you need: For example, you may already manage inventory with your ecommerce tool, but you need an HR platform to handle payroll.