The best ecommerce accounting software must integrate with your ecommerce platform to eliminate time-consuming duplicate entries and inevitable mistakes. Changes to inventory and sales recorded in your ecommerce software should flow automatically to your accounting software and vice versa. Here are the best accounting software for ecommerce businesses:
- QuickBooks Online: Best overall ecommerce accounting software with seamless ecommerce integrations and free ProAdvisor support for company setup
- Xero: Best for unlimited user access and strong project accounting and fixed asset management
- Zoho Books: Best for ecommerce companies looking for seamless Zoho integrations and robust mobile accounting
- Wave: Best free accounting and invoicing software for companies willing to use Zapier for ecommerce integrations
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The Fit Small Business mission is to provide small business owners with the best answers to their small business questions. We evaluated our best ecommerce accounting software by conducting an in-depth internal case study where our experts determine the strengths and weaknesses of each platform.
There are only two scenarios where we may recommend a solution that has not been subjected to our case study—if the software is not a complete bookkeeping system or if we don’t have access to evaluate the program. We evaluated all the platforms in this guide on the same set of criteria regardless of whether it is a partner company.
Best Ecommerce Accounting Software: Quick Comparison
QuickBooks Online: Overall Best Ecommerce Accounting Software With Seamless Ecommerce Integrations and Free ProAdvisor Support
Pros
- Direct integrations with Shopify, WooCommerce, Magento, and BigCommerce
- New subscribers can meet with a QuickBooks ProAdvisor to set up their new company for no charge.
- Connect with additional ecommerce apps through Webgility, A2X, Connex, and Parex Bridge
- Automatically applies sales tax based on transaction location and files sales tax returns
Cons
- More expensive than other small business accounting software
- Cannot handle complex ecommerce operations, like inventory management and order tracking
- QuickBooks Commerce works with QuickBooks Online only
Plans & Pricing
- Simple Start: $30 per month for one user
- Essentials: $60 per month for three users
- Plus: $90 per month for five users
- Advanced: $200 per month for 20 users
QuickBooks Online offers new customers the choice of 50% off for three months or a 30-day free trial.
QuickBooks Online earned the highest overall score in our case study—thanks to its enhanced accounting features, such as invoicing and inventory management, and extensive ecommerce platform integration. You can integrate it with major ecommerce platforms, such as Shopify, WooCommerce, Amazon, Magento, and BigCommerce. The best part is that it has built-in integration connectors for leading ecommerce platforms, like WooCommerce and Shopify while other software requires a third-party connector.
We also find QuickBooks excellent for mobile accounting. It allows you to complete various tasks, such as the ability to create and send invoices and accept payments from your smartphone. On the flip side, QuickBooks is less competitive in terms of pricing when compared to the other software on our list. Xero offers more affordable pricing while Zoho Books provides a free plan and Wave offers completely free accounting and invoicing services.
Are you running your ecommerce store on Amazon? You may want to check out our best accounting software for Amazon sellers.
Xero: Best for Unlimited User Access and Strong Project Accounting and Fixed Asset Management
Pros
- Direct integration with Shopify
- Integrate with third-party connectors A2X and Parex Bridge
- Good inventory accounting
- Much cheaper than QuickBooks and includes unlimited users in all plans
Cons
- Must manually set up sales tax rates for each location with a taxable sale
- Cannot file sales tax returns
- Few independent Xero-certified bookkeepers compared to QuickBooks
Plans & Pricing
All Xero plans include unlimited users:
- Xero Early: $15 per month for 20 invoices and five bills
- Xero Growing: $42 per month for unlimited invoices and bills
- Xero Established: $78 per month includes multiple currencies
Xero offers new users a choice between 50% off for two months or a 30-day free trial with no credit card required.
Xero is on a par with QuickBooks in terms of accounting features, but its ecommerce integration capability is not as seamless as that in QuickBooks. Xero has direct integrations with Zapier and Shopify, but you will need a third-party connector like Parex Bridge to integrate it with other platforms, such as WooCommerce, Amazon, and Etsy.
Our case study also reveals that Xero’s biggest weakness is limited customer support options—explaining its poor score in ease of use. The provider offers support only through email, a chatbot, and some self-help guides. Other providers like QuickBooks Online and Zoho Books offer phone support. which is crucial, especially for addressing integration and data syncing-related concerns. Its mobile app is also not as functional as QuickBooks and Xero, as it doesn’t allow you to accept payments from customers.
Another significant drawback to Xero compared to QuickBooks is the relatively small number of independent bookkeepers available in the US to help you manage your books.
Zoho Books: Best for Ecommerce Companies Looking for Seamless Zoho Integrations and Robust Mobile Accounting
Pros
- Integrates with other Zoho apps to provide a complete suite of management software
- Integrates with many ecommerce apps through Zoho Flows, which requires a separate subscription
- Zoho Inventory directly integrates with eBay, Shopify, Etsy, and Amazon
Cons
- No ecommerce integrations without subscribing to either Zoho Inventory or Zoho Flows
- Cannot determine sales tax rate by location or file sales tax returns
Plans & Pricing
- Free: $0 per month for one user and accountant for companies with annual revenues of $50,000 and below
- Standard: $20 per month for three users and 500 customers and vendors
- Professional: $50 per month for up to five users
- Premium: $70 per month for up to 10 users
- Elite: $150 per month for up to 10 users and advanced inventory control
- Ultimate: $275 per month for up to 15 users, 25 custom modules, and advanced analytics
Add-ons:
- Additional user: $3 per month
- Advanced autoscans for receipts: $10 at 50 scans per month
- Snail mail credits for sending physical invoices to customers: $2 per credit
As one of our best bookkeeping software for ecommerce businesses, Zoho Books has remarkable accounting features like QuickBooks and Xero. However, it excels in pricing and mobile accounting. It has a free plan—which can be a practical solution for ecommerce businesses that are just starting out. It even earned a perfect score in mobile accounting because it offers all of the features we wanted to see in a mobile app, including receipt capture, invoicing, and payment processing.
However, it took a hit in ecommerce integration due to its lack of built-in integrations. Unless you’re willing to use Zapier, you must purchase additional Zoho services, such as Zoho Inventory, which ranges from $0 to $329 monthly, or Zoho Flows, which ranges from $12 to $30 monthly.
In the interim, while we’re impressed with Zoho Books’ customer support, it’s not as easy to use as QuickBooks Online. It is a bit complicated and can be overwhelming for some ecommerce business owners with no accounting background.
Wave: Best Free Accounting and Invoicing Software for Companies Willing to Use Zapier for Ecommerce Integrations
Pros
- Has a free version for accounting and invoicing
- Can create and send an unlimited number of invoices
- Integrates with Zapier
- Lets you customize workflows using Zaps through Zapier
- Has good basic accounting features
- Has no direct ecommerce integrations or third-party connectors
- Can only add one user in the free plan
- Unable to connect bank accounts in the free version
- Has no project accounting and inventory features
- Cannot determine sales tax rate by location or file sales tax returns
Plans & Pricing
Wave offers two subscription options:
- Starter: Free; includes one user and basic accounting and invoicing features
- Pro: $16 per month when billed monthly or $170 per year when billed annually; includes unlimited user access, bank connections, and unlimited receipt scanning
Add-ons available for both Starter and Pro:
- Bookkeeping support through Wave Advisor: $149 monthly
- Accounting and payroll coaching: $379
- Assisted payroll services through Wave Payroll: $40 per month for tax service states and $20 per month for self-service states plus $6 monthly per employee
Receipt scanning: $11 monthly or $96 annually for Starter; included in Pro
Wave leads in pricing, as it offers a free plan for accounting and invoicing. You can send unlimited invoices to customers and keep track of your accounts at no cost—making it our best free accounting software. However, Wave scored poorly in all other criteria in our evaluation.
The program lacks inventory accounting, and any ecommerce integrations must be accomplished by creating Zaps with Zapier—which is very time-consuming compared to the direct ecommerce integrations offered by other software. The program itself is simple and easy to use, but we had to deduct some points because of its limited customer support options, particularly in the free plan. You can only access email support and live chat when you purchase a paid add-on (free users) or upgrade to the paid version.
How We Evaluated Accounting Software for Ecommerce Businesses
Using our expert-led case study, we evaluated the best ecommerce accounting software by focusing on six major criteria.
5% of Overall Score
Each software was rated on price compared to other software well suited to ecommerce companies. In addition to the cost of a monthly subscription, we factored in the number of available users and any additional charges that are likely incurred by ecommerce companies.
10% of Overall Score
The ease of use score is a combination of available customer support options, our subjective evaluation of the software’s ease of use, and the availability of third-party bookkeepers that support users of the software.
30% of Overall Score
We evaluated each software on banking, A/P, A/R, inventory, sales tax, and reporting.
5% of Overall Score
Mobile apps were evaluated on their ability to perform basic accounting functions from within the application.
50% of Overall Score
Accounting software was rated on its ability to integrate with ecommerce software, with direct integrations receiving more weight than integrations via a third-party connector. Through integrations, the software should synchronize inventory, A/R, and revenue.
Why Your Business Needs Ecommerce Accounting Software
Using accounting software for ecommerce provides numerous benefits, including the ability to:
- Integrate with ecommerce platforms, such as Shopify, Amazon, WooCommerce, and BigCommerce
- Manage your financial transactions, such as sales, expenses, and taxes, efficiently
- Track inventory levels in real time and calculate COGS automatically
- Categorize and track expenses so that you’ll know where your money is going
- Perform automatic sales tax calculations for easier tax reporting and compliance
- Generate reports, such as profit and loss (P&L), cash flow statements, and sales tax reports
Frequently Asked Questions (FAQs)
Features to consider when choosing ecommerce accounting software include invoicing, payment processing, expense tracking, financial reporting, inventory tracking, and integrations with your ecommerce platform.
Yes, Wave offers a free accounting software option for small businesses, but all ecommerce integrations must be done through Zapier.
Some ecommerce accounting software can integrate with popular ecommerce platforms, such as Shopify, WooCommerce, and Square. Be sure to check if the software you’re interested in offers integrations with your specific platform.
Bottom Line
It’s critical that ecommerce businesses invest in accounting software that integrates with their ecommerce platform to avoid unnecessary data entry and errors. For a well-rounded accounting software service, QuickBooks Online is our top pick—you’ll never go wrong with its features. Xero is also a great choice, although you may have trouble finding an independent Xero bookkeeper to work with you.