Ecommerce businesses face unique challenges that traditional accounting tools can’t always handle. Between juggling multi-channel sales, managing inventory across platforms, processing payments from different gateways, and tracking tax rules by region, it’s easy to lose time and accuracy in your books.
That’s why you need bookkeeping software that offers solutions specifically for online sellers. This includes automated sales tracking, inventory synchronization, multi-platform reporting, and integrated tax compliance tools. Let’s explore the different tools and features that make easy bookkeeping seamless for upcoming ecommerce entrepreneurs.
| Software | Price | G2 User Rating |
 Visit Wave | $0 monthlyAdditional tiers: $16 monthly | ★★★★ 4.3 out of 5 (based on 200+ reviews) |
| Verdict: Best for new ecommerce businesses | ||
 Visit QuickBooks Online | $35 monthlyAdditional tiers: $65, $99, and $235 monthly | ★★★★ 4.0 out of 5 (based on 3,000+ reviews) |
| Verdict: Best for growing ecommerce businesses | ||
 Visit FreshBooks | $21 monthlyAdditional tiers: $38, $65, and custom pricing | ★★★★ 4.5 out of 5 (based on 900+ reviews) |
| Verdict: Best for freelancers and solo ecommerce business owners | ||
 Visit Zoho Books | $0 monthlyAdditional tiers: $20, $50, and $70 monthly | ★★★★ 4.4 out of 5 (based on 300+ reviews) |
| Verdict: Best for mobile-first and multilingual ecommerce businesses | ||
 Visit Xero | $20 monthlyAdditional tiers: $47 and $80 monthly | ★★★★ 4.3 out of 5 (based on 700+ reviews) |
| Verdict: Most flexible accounting software for teams | ||
 Visit A2X | $29 monthly per platformMulti-channel tiers: $89, $115, $169, and $229 monthly | ★★★★ 4.9 out of 5 (based on 300+ reviews) |
| Verdict: Best for high-volume ecommerce businesses | ||
How to Choose Ecommerce Accounting Software
Choosing the best ecommerce bookkeeping software for your business isn’t just about price. You should find a solution that has the right features to provide real-time financial insights and works with your existing tech stack.
Inventory Management & COGS Tracking
For ecommerce business owners, managing inventory efficiently leads to accurate accounting and smooth operations. With features like real-time inventory sync, you can be sure that your stock levels are updated across all sales channels to prevent overselling and reduce stockouts. Ultimately, it affects customer satisfaction.
Meanwhile, accurate tracking of Cost of Goods Sold (COGS) helps you understand how much you’re spending on products. This way, you can implement better pricing strategies and improve profit margins.
Sales Tax Configuration
Managing sales tax across different states and countries can be overwhelming. Each region has its own tax laws, rates, and filing requirements. Manually keeping track of these variations is time-consuming and prone to errors. That’s why you should look for automated sales tax tools when choosing ecommerce accounting software.
Automated sales tax tools calculate the correct tax rates based on the customer’s location and the product type. They also handle reporting and filing to maintain compliance with various tax jurisdictions.
Ecommerce Platform Integration
Bookkeeping software that integrates with your ecommerce platform automatically syncs orders, payouts, and fees. This feature makes sure your financial records are always up-to-date and accurate, so you can make better decisions when it comes to money and growing your business.
Multi-Channel and Multi-Currency Support
If your ecommerce business sells to customers in different countries, you need accounting software that can handle multiple currencies and sales channels.
Customers prefer to see prices in their local currency. 92% of shoppers prefer to buy in their own currency, and 33% may abandon a purchase if prices are not displayed accordingly.
Accounting software with multi-currency support automatically converts foreign transactions into your home currency using real-time exchange rates. This helps you track profits accurately and simplifies tax reporting.
Automatic Bank Reconciliation
Manual bank reconciliation is time-consuming and prone to errors. By connecting directly to your bank accounts, the bookkeeping software can automatically match transactions and update your financial records in real-time. With instant transaction tracking, you can also spot any unusual spending or income patterns right away.
Receipt Scanning
Keeping track of paper receipts can be challenging for busy ecommerce entrepreneurs. Accounting software with receipt scanning allows users to capture and store receipts digitally.
You just need to take a photo of your receipt, and the software uses optical character recognition (OCR) technology to automatically extract key details like vendor, date, amount, and category. This feature simplifies small business expense tracking and ensures all expenses are accounted for during tax season.
Customer Support
The beauty of ecommerce is that your store is always open. One downside, though, is that financial issues can arise any time. That’s why having reliable customer support for your bookkeeping software becomes crucial. Tools like QuickBooks Online provide 24/7 phone and chat support, so you can get help when you need it.
Best Bookkeeping Software for Ecommerce Businesses
The right bookkeeping software makes running an ecommerce business easier by automating tasks, like syncing data and tracking costs. The best tools let you juggle sales, expenses, taxes, and inventory across platforms without a hitch.
Wave: Best Free Ecommerce Accounting Software
| Summary | |
| Wave is built for freelancers, small business owners, and ecommerce sellers who want basic tools to get started. While it doesn’t support inventory tracking or direct integration with platforms like Shopify or Amazon, it’s a strong starting point for ecommerce businesses on a budget. | |
| Pros | Cons |
| ✔️ Free to use ✔️ Simple dashboard for cash flow management ✔️ Supports unlimited invoices, estimates, and bookkeeping records ✔️ Multi-business support | ❌ No inventory tracking features ❌ No built-in ecommerce integrations like Shopify or BigCommerce |
Basic Features
Wave’s Starter Plan is completely free, making it ideal for early-stage ecommerce businesses. It allows you to:
- Create unlimited invoices, estimates, and bills
- Record bookkeeping entries for income and expenses
- Accept online payments with transaction fees (2.9% + $0.60 for credit cards)
- Use mobile apps for invoicing and cash flow tracking
- View sales tax info (entered manually)
- Access customer records and overdue invoice alerts
- See financial reports like profit & loss on a single dashboard
Pricing Plans
| Starter | Essentials |
| Free | $16 per month / $170 per year |
| Unlimited invoicing, estimates, basic reports, manual tax tracking | Everything in StarterAuto-import bank data, expense tracking, and remindersDigitally capture unlimited receipts |
Overview
Wave has a free plan, which makes it one of the best small business bookkeeping software options, including for ecommerce shops. It’s simple to use, doesn’t require deep accounting knowledge, and handles basic financial needs like income tracking, invoicing, and managing expenses.
While it lacks some tools that platforms like QuickBooks Online offer, such as inventory or tax automation, it’s still great for freelancers, sole proprietors, and side hustlers.
If you’re running a small Shopify store or selling products on Etsy and just need something to keep your records clean for tax season, Wave gets the job done. The mobile app is handy for creating invoices and checking cash flow when you’re on the go.
QuickBooks Online: Best for Growing Ecommerce Businesses
| Summary | |
| QuickBooks Online is a cloud-based accounting software that helps you manage income, expenses, taxes, and inventory with less manual work. This makes it a solid choice for small business owners and ecommerce sellers who want to scale efficiently, but it can have a high learning curve and pricing. | |
| Pros | Cons |
| ✔️ Works with Shopify, Amazon, WooCommerce, and BigCommerce ✔️ Auto-syncs ecommerce payouts and fees ✔️ Real-time inventory tracking ✔️ Native tools for sales tax tracking in multiple states | ❌ Higher tiers can be expensive ❌ Takes time to learn for beginners |
Basic Features
QuickBooks’ Simple Start plan starts at a monthly price of $35. It offers the following features:
- Track sales, refunds, rent, and supplies automatically
- Links your business bank account and tracks all deposits and expenses
- Auto-categorizes your income and expenses
- Lets you send customized invoices and accept online payments
- Flags potential tax-deductible expenses
- Generates key reports like Profit & Loss, Balance Sheet, and Expense Summary
- Tracks revenue from products and calculates how much sales tax you owe
- Tracks unpaid bills and payment due dates
Pricing Plans
| Simple Start | Essentials | Plus | Advanced |
| $35 per month | $65 per month | $99 per month | $235 per month |
| – Basic features – Track income and expenses – Bookkeeping automationInvoicing and payments – Sales tax tracking – Estimates – Receipt capture – Mileage tracking – Connect 1 sales channel – Bill management | – Everything in Simple Start – Up to 3 users – Manage bills and payments – Multi-currency support Enhanced reports | – Everything in Essentials – Up to 5 usersInventory tracking – Project profitability – Financial planning | – Everything in Plus – Up to 25 users – Batch invoices and expenses – Custom access controls – Workflow automation – Data sync with Excel – Revenue recognition – Premium support and training |
Overview
QuickBooks Online is perfect for ecommerce businesses that need to manage complex accounting and multi-channel sales for detailed financial reports. It automates bookkeeping tasks and connects directly to your ecommerce platforms, syncing orders, refunds, payouts, and fees in real-time.
You can also track inventory and products as you sell, which helps avoid stock issues. The software includes tools for auto-calculating sales tax based on your buyer’s location, which is crucial for ecommerce accounting.
Their Advanced plan adds features like batch invoicing, custom workflows, spreadsheet sync, and access for up to 25 users, which is ideal for scaling operations.
Additionally, QuickBooks Online lets you manage credit cards, send invoices, and track mileage, all in one place. While it’s pricier than tools like Wave or FreshBooks, it offers more for ecommerce businesses that are growing quickly.
FreshBooks: Best for Freelancers and Solo Ecommerce Business Owners
| Summary | |
| FreshBooks is an easy-to-use accounting software built for Etsy sellers, solo creators, and commission-based ecommerce businesses. However, it’s not ideal for inventory-heavy operations. | |
| Pros | Cons |
| ✔️ Easy time tracking and project billing ✔️ Payment reminders and online payment options ✔️ Expense tracking and receipt uploads | ❌ No inventory or product tracking ❌ Limited ecommerce platform integration |
Basic Features
FreshBooks is designed with simplicity in mind for solo business owners. Its key features let you:
- Send invoices to 5, 50, or unlimited clients, depending on plan
- Track income and expenses in real time
- Accept payments via credit cards and bank transfers (ACH)
- Create custom invoices, proposals, and estimates
- Generate time-tracking and tax-time reports
- Capture and store receipts by photo
- Give accountants secure access to your books
- Automate late payment reminders
Pricing Plans
| Lite | Plus | Premium |
| $21 per month | $38 per month | $65 per month |
| – Invoice up to 5 clients – Real-time expense tracking – ACH payments | – Up to 50 clients – Time tracking – Financial reports – Receipt capture | – Unlimited clients – Project profitability – Custom templates – ACH + card payments |
Overview
FreshBooks is ideal for freelancers and solo ecommerce business owners who offer custom or commission-based products and services. If you’re an artist, designer, or service-based seller using Etsy or managing direct client orders, this is one of the best accounting software tools for you.
You can create personalized invoices with your brand, track your time, and follow up with clients using automated payment reminders. It also helps organize your bookkeeping with photo-based receipt uploads and lets your accountant access your financial data easily.
FreshBooks doesn’t support inventory management or ecommerce platform integration like Shopify, though. Nonetheless, its project and time-based tools make it a smart option for service-first ecommerce businesses.
Zoho Books: Best for Mobile-First and Multilingual Ecommerce Businesses
| Summary | |
| Xero focuses on flexibility and team collaboration, with strong reporting, automated bookkeeping tools, and unlimited users. Although it lacks native Shopify integration and has limited tax automation, Xero still delivers solid value, especially with its low entry price and customizable dashboards. | |
| Pros | Cons |
| ✔️ Clean interface ✔️ Bulk reconciliation tools ✔️ Supports multi-currency accounting and inventory management | ❌ No direct Shopify or Amazon integration ❌ Advanced inventory and analytics cost extra |
Basic Features
Zoho Books comes packed with tools tailored for ecommerce business owners and freelancers who need control over finances and inventory:
- Create and send invoices, quotes, and sales receipts
- Accept online payments and manage recurring billing
- Reconcile transactions and automate bank feeds
- Enable client and vendor self-service portals
- Auto-scan receipts and track categorized expenses
- Generate over 50 financial reports (P&L, Balance Sheet, etc.)
- Track mileage and 1099 contractors
- Manage tax deductions, W-9s, and 1099 filings
- Get reorder alerts using barcode or SKU-based tracking
- Build custom workflows and approval steps
- Add multiple users and assign specific roles
Pricing Plans
| Early | Growing | Established |
| $20 per month | $47 per month | $80 per month |
| – 20 invoices/quotes5 bills – Bank reconciliation – Basic reporting | – Unlimited invoices – Expense capture – Short-term cash flow tracking | – Multi-currency support – Project tracking – Expense claims – Inventory (add-on) |
Overview
Zoho Books is the best accounting software for ecommerce businesses that need mobile-first access and support for global clients. It’s especially useful for sellers who manage inventory with barcodes or SKU codes and want control over taxes and project finances. With built-in support for client and vendor portals, it’s also a good fit for teams that regularly collaborate with contractors or suppliers.
If you’re running a multi-country ecommerce store or working with international clients, Zoho’s multi-currency support and multilingual UI will help you operate smoothly.
The Premium plan includes budgeting, automation tools, and custom functions for advanced accounting workflows. Although it doesn’t connect natively with platforms like Shopify or Amazon, it shines in customization and mobile tools, making it a strong contender for ecommerce businesses ready to grow.
Xero: Best Accounting Software for Teams and Flexibility
| Summary | |
| Zoho Books is ideal for ecommerce businesses with global clients thanks to its multilingual interface, customizable reports, and inventory tracking. It may require some onboarding time, though, and offers fewer integrations compared to QuickBooks Online or Xero. | |
| Pros | Cons |
| ✔️ Multilingual support for international ecommerce ✔️ Barcode-based inventory and SKU tracking ✔️ Strong automation and approval tools ✔️ Affordable entry pricing with wide feature set | ❌ Fewer third-party ecommerce integrations ❌ Learning curve for customization and modules |
Basic Features
Xero offers a full set of tools for small ecommerce businesses and teams, including:
- Sending unlimited invoices and quotes (or 20 in entry plan)
- Entering and reconciling bills and bank transactions
- Capturing receipts and bills with Hubdoc
- Managing cash flow and tracking business performance
- Automating bill payments and view payment timelines
- Setting up W-9 and 1099 forms for contractors
- Tracking and calculating sales tax
- Using multi-currency accounts for international clients
- Claiming business expenses and reimbursements
- Adding inventory tracking with optional add-on
- Getting short-term financial snapshots and projections
Pricing Plans
| Free | Standard | Professional | Premium |
| $0 | $20 per month | $50 per month | $70 per month |
| – Invoicing – Mileage tracking – 1099 support – Basic reports1 user + accountant | – Recurring invoices – Tax toolsBank feeds – Report tags – API access – 3 users | – Vendor billing – Project tracking – Inventory – Time sheets – Approvals – 5 users | – Budgets – Fixed asset tracking – Domain setup – Full workflow automation – 10 users |
Overview
Xero is best if you have a team since they can easily track payments, reconcile orders, and update inventory together. It features reliable project tracking, real-time dashboards, and built-in support for bills and contractor payments, which are important for ecommerce businesses that outsource fulfillment or marketing.
While it lacks native Shopify or Amazon integration, third-party apps can help bridge that gap. If you need flexibility, like advanced reporting and collaborative workflows, Xero is a strong pick.
A2X: Best for High-Volume Ecommerce Businesses
| Summary | |
| A2X is not an all-in-one accounting software, but it syncs platforms like Amazon and Shopify with QuickBooks Online or Xero. It transforms raw payout data into clean summaries for sales, refunds, fees, and taxes to match your bank deposits perfectly. | |
| Pros | Cons |
| ✔️ Auto-summarizes ecommerce transactions for reconciliation ✔️ Tracks Cost of Goods Sold (COGS) for accurate financials ✔️ Connects directly to Shopify, Amazon, Etsy, Walmart, and eBay | ❌ It’s an add-on tool, not standalone accounting software ❌ No invoicing, billing, or tax filing tools built in |
Basic Features
A2X fills the gap between selling platforms and accounting software. Here’s what it offers:
- Auto-sync ecommerce payouts, refunds, sales tax, and fees
- Summarize transactions into accurate journal entries
- Assign tax rules for each transaction type and region
- Match payouts to bank deposits in QuickBooks or Xero
- Track and reconcile COGS
- View order and financial history at any time
- Use for multiple ecommerce sales channels
- Get support via email, live chat, and 1:1 onboarding
Pricing Plans
A2X has specific pricing for different platforms, like Amazon, Shopify, Etsy, and eBay. Most start at $29 monthly, except for Walmart, which starts at $79 per month.
It also offers plans for multi-channel support, which helps online sellers consolidate their financial data from different marketplaces into a single accounting workflow.
| A2X Multi 1K | A2X Multi 2K | 2X Multi 5K | A2X Multi Premium 10K |
| $89 per month | $115 per month | $169 per month | $229 per month |
| – 1,000 orders/month – 2 sales channels – Email and live chat support – Track COGS and financial history | – 2,000 orders/month – 3 sales channels – Email and live chat support – Same as A2X Multi 1K with more channels | – 5,000 orders/month – 4 sales channels – Premium support – 1:1 onboarding – Track COGS and history | – 10,000 orders/month – 5 sales channels – Premium support – Full feature set, high-volume scale |
Overview
If you’re running a high-volume ecommerce business and use platforms like Amazon or Shopify, A2X connects your ecommerce activity to your accounting software.
It works with QuickBooks Online, Xero, Sage, and NetSuite to automate the flow of ecommerce data into your books. It doesn’t replace your bookkeeping software, but it makes ecommerce accounting smoother by eliminating manual entry and making sure your records are accurate down to the penny.
A2X is especially useful for ecommerce businesses with lots of products or marketplaces, and it’s built to handle thousands of orders per month. It supports COGS, multiple channels, and provides solid financial visibility to help you grow.
It does lack core features like invoicing and bank reconciliation. However, it wins when it comes to ecommerce transaction accuracy and time savings.
Find the Right Fit for Your Ecommerce Accounting Needs
Running an ecommerce business is already a lot of work. Your bookkeeping shouldn’t make it harder. Finding the right ecommerce accounting tool helps you avoid financial mistakes and make better decisions about your money.
If this all sounds too overwhelming, you’re not alone, and you don’t have to figure it out by yourself. Experts at EpicBooks provide bookkeeping services tailored for ecommerce businesses, helping you focus on growing your store, not your spreadsheets.
FAQs
What’s the difference between regular bookkeeping and ecommerce bookkeeping?
Regular bookkeeping tracks basic business finances, like income, expenses, and invoices. It works fine for local shops or service providers. But ecommerce bookkeeping needs more.
If you sell online, you’re likely dealing with different platforms (like Shopify, Etsy, or Amazon), payment processors (like Stripe or PayPal), and multiple sales channels. You might even sell internationally, which adds currency conversions and extra tax rules.
Ecommerce bookkeeping also tracks inventory, shipping costs, fees, and refunds, usually across several tools. A good ecommerce bookkeeping system automatically syncs all these pieces to help you avoid errors and give you a full picture of your business performance.
For example, when you sell on Amazon, they deduct fees before sending you a payout. Basic bookkeeping might just show what hits your bank. However, ecommerce bookkeeping breaks that down to show sales, shipping, fees, and taxes separately for accuracy.
What is the best accounting method for ecommerce business?
If you’re torn between using cash vs accrual accounting for your ecommerce business, it’s best to use the latter. Cash accounting records income only when you get paid and expenses only when you pay bills. It’s simple, but it doesn’t always reflect your real profits, especially with inventory and sales happening at different times.
Accrual accounting records income when you make the sale, not when the money hits your account. It also records expenses like inventory when it’s used, not when you pay for it.
This method gives a more accurate view of your ecommerce finances, especially if you’re dealing with returns, delayed shipping, or bulk inventory purchases.
For example, if you buy $5,000 worth of inventory in January but don’t sell it until March, cash accounting would show a big loss in January and a big gain in March. Accrual accounting adjusts entries and spreads that cost out to match your actual sales, so you can manage your profits better.
If you’re just starting out and your store is small, cash basis might work at first. But once you have inventory, multiple sales channels, or want to grow, switching to accrual is best.
Is it necessary to hire a bookkeeper if I’m using ecommerce accounting software?
Ecommerce accounting software is helpful, but it doesn’t replace a bookkeeper. Software tracks data, while bookkeepers make sure it’s right, organized, and useful. They can spot errors, give financial advice, and help you understand what’s really going on in your business.
Bookkeepers know how to categorize complex ecommerce transactions, match payouts with orders, and track returns, fees, and chargebacks. If your business is growing or you feel overwhelmed, a bookkeeper can save you hours and help you avoid costly mistakes.
If you want to grow your business, outsource bookkeeping to experts like those in EpicBooks, who provide services tailored to online sellers, such as reconciling sales from platforms like Shopify and Amazon and making your books tax-ready.
What reports should I review regularly to keep my ecommerce finances healthy?
The most important reports ecommerce businesses should check are their profit & loss (P&L) statement, balance sheet, cash flow statement, COGS report, and sales tax summary.
The P&L statement, also known as the income statement, shows how much you earned, what you spent, and your total profit or loss. It’s used to track how your store is doing overall. The balance sheet, on the other hand, shows your assets (like cash and inventory), liabilities (like credit card debt), and your business’s net worth.
The cash flow statement tracks money coming in and going out. It helps you plan for bills, avoid cash crunches, and decide when you can afford new investments.
Meanwhile, the COGS report shows how much it costs to produce the products you sell. You need this information to calculate your true profit margins and plan accordingly.
Lastly, the sales tax summary helps you stay on top of what you owe and when to file, especially if you’re selling in different states or countries.
How can bookkeeping help my ecommerce business grow faster?
Good bookkeeping lets you make faster, smarter business decisions. You know how much inventory to order, which products are most profitable, and when it’s safe to invest in ads, staff, or new tools.
You can also catch problems early. For example, if you’re spending too much on shipping or certain products aren’t selling, your books will show you. That way, you can fix it before it hurts your bottom line.
Having clear financial records also makes it easier to get loans or funding. Lenders and investors want to see that your business is stable and profitable.
Bookkeeping helps you stay tax-ready, too. No more missing receipts or guessing at deductions. At tax time, your accountant will thank you, and you’ll likely save money.
