5 Best Accounting Software for E-commerce 2025

In selecting the best accounting software for e-commerce businesses, I recommend one that can sync transactions between the e-commerce platform and accounting software, track multi-channel sales, reconcile payments, handle sales tax, and automate COGS and returns for accurate reporting. With that in mind, here are the software that made it to my list:

Quick comparison of the best accounting software for e-commerce

My evaluation

QuickBooks Online earns high marks for both accounting and e-commerce functionality. Its strength in accounting is expected, given its versatility, but what stands out is its e-commerce adaptability. While not an e-commerce platform itself, QuickBooks Online integrates directly and via third-party apps with major e-commerce platforms. The built-in Mailchimp integration within Intuit also makes abandoned cart email automation seamless.

Moreover, it did well in ecommerce features due to its strong integrations and automation but lost points for lacking built-in abandoned cart tracking and advanced marketplace reporting. While it syncs with Shopify, Amazon, and eBay, multi-channel sellers may need third-party apps like A2X for detailed revenue attribution and reconciliation. Despite this, it remains a top choice for small or midsize businesses.

The main drawback of QuickBooks Online is scalability, as it limits the number of seats to a maximum of 25. If you need more users, Xero might be the better option. But if you need more seats and have outgrown QuickBooks, I highly recommend Sage Intacct.

Read our QuickBooks Online review

Pros and cons

Xero: Best for growing companies with multicurrency needs

My rating: 4.2 out of 5

Xero is my pick for growing companies because it provides unlimited seats in all plans. On top of that, it offers outstanding features in multicurrency transactions, making it a great pick for e-commerce businesses with international transactions.

It also integrates with Shopify, Amazon, WooCommerce, BigCommerce, and more via third-party apps like A2X, Webgility, and Synder. These integrations automate sales data syncing, tax calculations, and COGS tracking. Its bank feeds and automatic reconciliation streamline payment processing from Stripe, PayPal, and other gateways, reducing manual work.

Pricing

• Early: $20 per month (limited to 20 invoices and five bills)
• Growing: $47 per month
• Established: $80 per month

Get 90% off for three months when you sign up, or try a plan for 30 days and pay the regular rate after the trial.

My evaluation

Xero goes head-to-head with QuickBooks Online but stands out for scalability and global e-commerce support. Unlike QuickBooks, it allows unlimited users, making it ideal for growing businesses needing access for accountants, finance teams, and e-commerce managers.

Another key advantage is its multicurrency support. It automatically converts transactions in over 160 currencies with real-time exchange rates, which is essential for international sales on platforms like Amazon, Shopify, and eBay.

However, Xero didn’t score as high in e-commerce features because its integration options and reporting capabilities aren’t as polished. The platform’s editor lacks flexibility, making it frustrating to customize reports or streamline workflows for e-commerce businesses. Additionally, Xero is less popular in the US, where QuickBooks Online dominates the market. Many US CPAs and bookkeepers are QuickBooks ProAdvisors, making QuickBooks Online ideal for businesses wanting to outsource their bookkeeping.

Read our review of Xero

Pros and cons

Zoho Books: Best for automation and customization

My rating: 4.1 out of 5

Zoho Books is tightly integrated within the Zoho ecosystem, making it a great choice for e-commerce businesses using Zoho Commerce, Zoho CRM, or Zoho Inventory. Its built-in automation reduces manual work and seamless data syncing keeps financials updated across platforms.

With multiple integrations within the Zoho environment, it gives businesses centralized control over sales, accounting, and inventory. Features like automated invoicing, tax tracking, and order management simplify e-commerce operations. Though it lacks direct Amazon or eBay integrations, tools like Zapier and Zoho Flow help bridge the gap, making it a flexible and automation-friendly option for e-commerce sellers.

Pricing

• Free: For one user only
• Standard: $15 per month for three seats
• Professional: $40 per month for five users
• Premium: $60 per month for 10 seats
• Elite: $120 per month for 10 users
• Ultimate: $240 per month for 15 seats

Additional seats cost $11 per user, per month.

My evaluation

Zoho Books earns a high mark in accounting features — no surprises there. However, its e-commerce features took a hit due to the lack of direct integrations with major e-commerce platforms. While Zoho Books integrates with Zoho Commerce, that isn’t a primary platform in my evaluation, though I still awarded extra points for it.

What truly sets Zoho Books apart, though, is its outstanding customer support, which outperformed many competitors. You can contact the team via phone, email, and live chat, while an extensive knowledge base is available for quick answers.

Though Zoho Books offers integrations with other Zoho apps, there’s a lot of competition in the market that may steer you away from Zoho’s other offerings. If you have no plans to stay within the Zoho app ecosystem, I recommend going with Xero because it provides more flexibility with third-party integrations, stronger multi-currency support, and unlimited user access.

Read our Zoho Books review

Pros and cons

Sage Intacct: Best for multi-entity companies

My rating: 3.9 out of 5

Sage Intacct is a solid pick if your company manages multiple organizations. Because of its built-in consolidation features, Sage Intacct makes accounting for intercompany transactions easy. It automates eliminations, multi-entity reporting, and currency conversions, reducing the manual work typically required for consolidated financials.

Beyond its strength in multi-entity management, Sage Intacct also excels in advanced financial reporting, offering customizable dashboards and deep analytics for e-commerce businesses handling high transaction volumes. Its automation capabilities extend to inventory tracking, order management, and revenue recognition, making it well-suited for large-scale e-commerce operations.

Pricing

Contact Sage for a custom quote.

My evaluation

Overall, Sage Intacct performed well. It’s the only provider that aced my assessment of accounting features, excelling in revenue management and multi-entity accounting. That makes it a strong choice for e-commerce businesses needing advanced financial tools.

It scored lower in e-commerce features due to its lack of direct integrations with Shopify, Amazon, and eBay, relying on third-party connectors that add complexity and cost. It also lacks native abandoned cart tracking and multi-channel revenue attribution, requiring additional software to fill these gaps. While its automation and reporting are strong, the absence of built-in e-commerce tools makes it less ideal for sellers needing seamless platform connectivity.

Moreover, it only scored only above average in ease of use, mainly due to limited bookkeeping support in the US. While Sage Advisors are available, the network isn’t as widespread as QuickBooks ProAdvisors, which still dominates the market.

Read our review of Sage

Pros and cons

Wave: Best for new e-commerce sellers

My rating: 3.3 out of 5

If you’re just starting your e-commerce store and have fewer sales, Wave is the perfect simple accounting solution for tracking e-commerce income and expenses. Since it’s free, it’s ideal for businesses wanting to keep costs low while managing basic bookkeeping. If you’re an e-commerce seller who sells part-time and has no plan of scaling up, choosing Wave is a cost-effective option.

Pricing

• Starter: Free for one user
• Pro: $16 for unlimited users

My evaluation

Wave has a “glass ceiling” in terms of capabilities and long-term use. It offers simple accounting features that work for small e-commerce stores or casual sellers. However, it lacks built-in COGS tracking, which can be challenging for businesses handling high sales volumes. For smaller stores, tracking COGS manually in a spreadsheet may still be manageable.

The platform also has limited e-commerce integrations, so don’t expect automated inventory syncing, multi-channel revenue tracking, or advanced sales tax automation. If you want to stay free but have the option to upgrade and scale, I recommend picking Zoho Books. Its free tier is great for casual e-commerce.

Read our Wave review

Pros and cons

How I evaluated the best e-commerce accounting software

I used a rubric to evaluate the five best accounting software for e-commerce businesses.

Pricing (10% of overall score)

This breaks down the true cost and value of accounting software, ensuring you get value for money. The base subscription and additional user costs are measured against affordability, with higher scores awarded to a program that keeps pricing reasonable. Additionally, the features-to-cost ratio reveals whether a tool’s price tag is justified by its capabilities, rewarding those that deliver strong functionality without inflating costs.

Accounting features (40% of overall score)

My assessment focuses on core accounting capabilities, including transaction management, financial reporting, and automation. I review how well the software supports e-commerce businesses, particularly in areas like tax compliance, inventory tracking, and multi-entity accounting. Usability, customization, and scalability are also key factors, ensuring the tool meets the needs of growing businesses.

E-commerce features (20% of overall score)

This focuses on platform integrations, payment reconciliation, and transaction automation to ensure seamless financial tracking. I examine how well the software handles abandoned cart tracking, revenue attribution, and returns management, helping you optimize sales and profitability. Additionally, I consider multi-channel sales support and reporting accuracy, ensuring you can track performance across different platforms and marketing sources.

Ease of use and support (20% of overall score)

I evaluate usability, support, and accessibility, ensuring you can efficiently manage accounting processes. I also review bookkeeping support, dashboard navigation, and learning curve, focusing on how intuitive the software is and how easily you can set up and integrate e-commerce platforms. Additionally, I examine customer support quality, including response times, available resources, and the accessibility of certified bookkeeping professionals.

User reviews (10% of overall score)

I also take user feedback from G2 and Capterra into consideration. I use the weighted average scores of those two review sites as a basis for the user review score.

Ratings

I gave the following base ratings to score software.

• Excellent (5): The feature is fully developed, highly automated, and seamless. It requires little or no manual effort, integrates smoothly with other systems, and includes advanced capabilities that improve efficiency or provide extra value beyond basic expectations.
• Very Good (4): The feature is well-designed and effective but has minor limitations that may require occasional expert adjustments. It works reliably and includes most expected functionality but may lack some refinements or advanced settings.
• Good (3): The feature meets basic requirements but has noticeable gaps that could impact usability. It functions as expected but requires some manual work or expert input to operate efficiently. It’s usable but not the best in its category.
• Fair (2): The feature exists but is underdeveloped or lacks key functions. It may be difficult to use, require frequent workarounds, or rely heavily on expert tweaks to perform essential tasks. It is functional but frustrating or incomplete.
• Poor (1): The feature is barely usable, unreliable, or does not perform as intended. It may have significant limitations, have frequent errors, or lack key integrations, making it impractical for real-world use.
• N/A (0): The feature is completely missing from the software, meaning users must rely on third-party solutions, workarounds, or manual processes to compensate for its absence.

In addition to the base rating, I applied expert adjustments, adding 0.1 to 0.5 points based on key strengths or enhancements that improve functionality. These adjustments fine-tune the scores to reflect usability, efficiency, and harmony if combined with other features.

Frequently asked questions (FAQs)

Is QuickBooks good for an e-commerce business?

Yes, it is. It integrates with Shopify, Amazon, eBay, and other platforms, automates sales tax tracking, and simplifies COGS tracking, multi-channel revenue reporting, and payment reconciliation. Its third-party app marketplace also expands functionality for inventory management and advanced analytics.

Which accounting software is best for Shopify?

QuickBooks Online, Xero, and Zoho Books are top choices for Shopify, depending on business size and needs. QuickBooks Online offers direct integration, automated sales tracking, and strong financial reporting. Meanwhile, Xero is optimal for multicurrency support and automation, whereas Zoho Books is ideal for businesses already using Zoho’s ecosystem and needing affordability with automation.

What is the best accounting software for Amazon sellers?

QuickBooks Online, Xero, and Sage Intacct stand out. QuickBooks Online integrates with Amazon Seller Central via apps like A2X, making sales reconciliation and COGS tracking seamless, while Xero is a strong alternative with multicurrency support and automated bank feeds. Sage Intacct is ideal for high-volume Amazon sellers needing advanced inventory management and multi-entity accounting.