The Best Ecommerce Accounting Software in 2024

Get the tools you need to manage your small business finances with this guide to the best ecommerce accounting software available in 2024.

Bookkeeping and accounting can be tedious and confusing—especially as a new small business owner. Luckily, a host of ecommerce accounting software solutions can help you efficiently and accurately accomplish tasks like expense tracking, payroll, and tax prep. The best accounting software makes it easy to analyze your cash flow, helping to support the overall financial health of your ecommerce business.

The proliferation of AI technology is also making it simpler than ever to save time and streamline your small business accounting tasks. “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.”

We’ve rounded up seven great accounting software recommendations to help you find the best accounting solution for your ecommerce business.

7 best ecommerce accounting software solutions

1. QuickBooks Online
2. Wave
3. Zoho Books
4. FreshBooks
5. Sage 50
6. Xero
7. A2X

Below, take a look at seven ecommerce accounting solutions that can help keep your business on the right track. Whether you’re just starting out as a solopreneur or managing a growing ecommerce company, the ideal accounting software for your business needs is out there.

1. QuickBooks Online

You may have already heard of the class accounting software QuickBooks. This tried and true double entry accounting software counts more than 1.4 million businesses as customers. Today’s version of the small business accounting software is available online (as opposed to desktop application only), and it features AI capabilities. Those features include automated late payment reminders, personalized invoices, and expense report automation, in which you simply send the AI a photo or email detailing an expense, and it enters it into your books.

QuickBooks’s cloud-based accounting software has a simple interface that provides small business owners with essential functionality like cash flow view, invoice generation, and bookkeeping automation, all available at the lowest price bracket ($35/month). It also boasts hundreds of third-party software integrations, which are available at all price tiers, including a Shopify integration, which can automatically import orders and payouts from your online store to your QuickBooks account.

Note you’ll need to level up to access services like multiple currencies transactions and the ability to attach billable hours to projects. Inventory tools are available, too, but only in QuickBooks Plus and Advanced packages.

Pricing:

• $35/month for Simple Start (automated bookkeeping, basic reports, auto-calculated sales tax).

• $65/month for Essentials (facilitates multiple currencies transactions, connects three sales channels, provides detailed reports, and more).

• $99/month for Plus (additional features like profit projections, financial plan generation, and inventory management and tracking).

• $235/month for Advanced (high-level tools geared toward larger companies, including 25-user collaboration, automated workflows, and unlimited custom reports).

2. Wave

Every dollar counts when you’re getting your ecommerce business off the ground, so you might be reluctant to fork over hundreds of dollars per year for accounting software. If this sounds like you, consider Wave, which offers one of the best free accounting software plans on the market. Their free accounting software starter plan includes the basic services you’ll need to keep growing your small business: You can create unlimited invoices and bookkeeping records, accept online business payments, and send invoices.

If you need more functionality, you can opt for Wave’s Pro Plan for $16/month. This version of the tool offers accounting features that help you save time through automation: It can auto-import bank transactions, merge and categorize those financial transactions, and automate late payment reminders. It can also digitally capture your receipts, saving you even more time. Note that neither free nor paid versions of Wave include a Shopify integration.

Pricing:

• Free for Basic (unlimited estimates, invoices, and bookkeeping records).

• $16/month for Pro (automated bank transactions import and late payment reminders, digital receipt capture, and more).

3. Zoho Books

Zoho Books offers a free version of its online accounting software to companies that earn less than $50,000 in annual revenue. That makes it a great choice for new ecommerce business owners with tight budgets. Beyond affordability, Zoho Books is known for its mobile accounting app, which adds convenience for business owners who don’t spend their day at a desk.

Zoho Books integrates with many online payment gateways, like PayPal and Stripe, and includes inventory tracking features—in addition to standard accounting features like invoice generation and expense tracking and categorization. You can also cut down on your time spent bookkeeping and accounting by auto-completing tasks like sending emails and filling out fields. Zoho Books offers a Shopify integration through its product Flow, but you’ll need to pay an additional $25 or $41 per month to access it.

Pricing:

• Free for businesses with less than $50,000 in annual revenue (basic bookkeeping and accounting tools).

• $20/month for Standard (additional tools including custom financial reports and fields, bank feed connection, and sales tax tracking).

• $50/month for Professional (more features like multi-currency transactions, timesheet billing, inventory tracking).

• $70/month for Premium (higher level accounting tools including budget management, cash flow forecasting, and the ability to design custom accounting functions).

4. FreshBooks

FreshBooks is an affordable accounting software for those who prioritize ease-of-use. The lowest priced Lite plan runs just $19/month, and it has everything you’ll need to invoice customers and handle basic accounting tasks like tracking expenses and income. Two notable limitations at the lowest price point is the number of billable clients you can have (which maxes out at five) and collaborators (all of which entail an additional fee of $11/person).

The program’s Plus and Premium plans ($33/month and $60/month) offer increasing levels of automation. That includes the ability to automate emails (like late payment reminders or successful payment confirmations) and profit projections—and the Select version (price upon request) has a robust feature set that includes lower credit card transaction fees and the ability to create two user accounts for free. Note that FreshBooks’ inventory management system is less sophisticated than other small business accounting software solutions, so it might be better suited to service-based businesses than ecommerce businesses.

Pricing:

• $19/month for Lite (unlimited invoices to five clients and basic services like expense tracking).

• $33/month for Plus (unlimited invoices to 50 clients and automations like receipt capture).

• $60/month for Premium (unlimited invoices to unlimited clients and increased customization and automation capability).

• Price upon request for Select (lower bank transfer and credit card fees, access to select customer service, the ability to set up recurring invoices and client retainers, and more).

5. Sage 50

Sage 50 is a more advanced accounting software—and comes with a higher price point. With its lowest price tier at $625/year (around $52/month), it’s more expensive than many other accounting software options, making it best for businesses with more complex needs.

Sage 50’s stand-out features include financial forecasting tools you can use to run what-if scenarios, job costing tools that show you how much various projects and jobs at your company cost versus how much money they bring in, and inventory management features that show you what’s in stock and what’s on order. It also features AI technology that can identify ledger errors and reduce time spent on manual data entry.

One significant limitation is that not all of these tools are available at the lowest price tier. Another is that it lacks a Shopify integration. Sage 50 is a desktop software, but it does offer cloud connectivity like online financial data backup through Microsoft 365.

Pricing:

• $625/year for Pro (one user and features including automated bank reconciliation, invoice and bill tracking, and job costing).

• $1,043 for Premium Accounting (1–5 users, industry-specific functionality, and multi-company integration).

• $1,780 for Quantum Accounting (1–40 users, workflow management, and role-based user permissions).

6. Xero

Xero knows its audience—small businesses and startups—and serves them well with a few key features. One, it offers access to onboarding specialists during the first 90 days of creating your account. Two, it prioritizes ease of use with a minimalist design tailor-made for non-accountants. If you’re a Shopify merchant, there’s additional benefit, as it seamlessly integrates with Shopify.

All plans offer services including W-9 and 1099 management and short-term cash flow and business snapshots, but other essential services like bulk expense tracking are only available in the higher price tiers (starting at $42/month).

Pricing:

• $15/month for Early (five bills, 20 invoices, and basic features like bank transaction reconciliation).

• $42/month for Growing (unlimited bills and invoices, plus bulk reconciliation).

• $78/month for Established (additional features including multi-currency transactions, project tracking, and expense claiming).

7. A2X

A2X isn’t a full-service accounting software, but it’s still a great tool for ecommerce business owners (plus, it’s specifically designed for ecommerce businesses). A2X ecommerce accounting software integrates with major ecommerce platforms (including Shopify) and your accounting software (if your accounting software is Xero, QuickBooks Online, or Sage). Ultimately, A2X can help you out with all the particularities that can make ecommerce accounting so tricky, like VAT rates, sales tax, shipping costs, and more.

Pricing:

• For integrations with Shopify, Etsy, Amazon, and eBay, $29/month (up to 200 orders per month) to $115/month (up to 5,000 orders).

• For integration with Walmart, $79/month (up to 2,000 orders per month) to $229/month (up to 15,000 orders).

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

How to choose the best accounting software for your ecommerce business

• Outline your current and future accounting needs
• Consider your current budget vis-a-vis expected growth
• Consider third-party integrations

There’s a lot to consider when you’re deciding on the best accounting software for your ecommerce business. Are you looking for a simple cloud-based accounting solution that automates pesky bookkeeping tasks like logging receipts? Or are you in the market for a more extensive ecommerce accounting software solution that can generate business performance reports, help you manage inventory, and project your small business’s profitability?

The following considerations will help you hone in on what the right small business accounting software needs are for your business.

Outline your current and future accounting needs

Your choice of software will first and foremost be informed by your needs. Run down the following list of considerations to assess your priorities:

• Will you be the only one using the software or do you need to add other collaborators? Do you currently or expect to work with an accountant who may have their own preferences on the choice of software?

• How many expenses do you typically incur each month? Will you be dealing with receipts in bulk?

• Do you need to generate customer invoices each month? Approximately how many invoices might you be creating and sending out?

• How familiar are you with accounting concepts and interfaces? Do you need something easy to use, or can you handle more complexity?

• What accounting tasks do you currently spend a lot of time on, or expect to spend time on? Where could automations save you time?

• Do you need third-party integrations—for example, with Shopify?

• Do you need additional functionality like inventory management, employee time tracking, or financial forecasting?

Consider your current budget vis-a-vis expected growth

Every penny counts when you’re getting your ecommerce business up and running, and you might not be in a position to spend hundreds (or thousands) of dollars a year on an ecommerce accounting software. That said, consider the capability ceiling—that is, it’s ability to meet your needs as your business (and therefore your budget) grows. Think about how much and how quickly you intend to grow, and consider whether your chosen software offers upgrades that can facilitate your growth. If it doesn’t, you could be forced to migrate softwares, which will come with a cost and potentially a whole new learning curve.

Consider third-party integrations

If you’re a Shopify merchant, you can connect your store with accounting software like QuickBooks, Zoho Books, or Xero. A seamless integration with ecommerce accounting software eliminates the need for manual data entry. That’s valuable because entering financial data yourself might elevate your risk of making mistakes, so accounting integrations can help mitigate those risks.

Accounting software FAQ

What is the most commonly used accounting software?

QuickBooks is fairly ubiquitous among small business owners and the accountants who support them. It’s been around for decades and is the top pick by almost all major accounting software reviewers.

Why is QuickBooks best for small business?

QuickBooks is generally considered the industry standard in accounting software for small businesses. It is relatively easy to use and provides essential bookkeeping and accounting functionality like expense tracking, financial statement generation, and invoicing.

Which accounting software is the cheapest?

Wave and Zoho Books both offer free accounting software plans. Beyond that, Xero and FreshBooks offer packages for $15 and $19 per month, respectively.