Accounting Software for Online Sellers

If you’re still using Excel or Google Sheets for bookkeeping, it might be holding your online business back. Switching to dedicated accounting software automates tasks, cuts down errors, and gives you real-time financial insights, setting your business up for success and growth.


Perhaps these facts can give you an idea of the opportunities you’ve been missing:


  • Companies using accounting software cut manual data entry errors by up to 90%, making financial reports more accurate and saving time on corrections.
  • Automating accounting tasks lets businesses handle up to 75% of their processes without manual work, freeing up time for strategic activities.
  • Over 64% of small business owners using accounting software report better financial management and more confidence in their data.
  • Businesses often see revenue boosts by using automated invoicing and payment tracking, which helps manage receivables and improve cash flow.
  • Entrepreneurs find accounting software invaluable during business growth, as it helps manage financial complexities and focus on scaling.


Wondering which accounting software to use? With so many choices, finding the perfect fit for your business can be tricky. You need one that's powerful enough to handle big data, automate complex tasks, and scale with your business.


Here are the top 10 accounting software options ideal for online stores on platforms like Shopify, WooCommerce, BigCommerce, and Amazon. I've personally used some of these and can vouch for their capabilities.


Let’s check them out!


Zoho Books


Managing your finances has never been easier with Zoho Books. This cloud-based software takes care of everything in your accounting workflow, from invoicing and billing to inventory management and bank reconciliation.


With Zoho Books, you can easily generate detailed financial reports, calculate and file taxes, handle transactions in multiple currencies, and track billable hours by project. Plus, if you're already using other Zoho applications like Zoho CRM, Zoho Inventory, or Zoho Projects, it integrates seamlessly with them.


Zoho Books is powered by Zia, Zoho's AI tool. Zia automates reminders, detects anomalies in financial transactions, and provides predictive analytics. This means a more streamlined workflow and fewer repetitive tasks for you.




Business accounting can be tricky, even for the pros. But what if I told you there’s software designed specifically for non-accountants? Meet Kashoo. It’s made for business owners who find finances overwhelming.


Kashoo is cloud-based, so you can access your financial data anywhere, anytime. It uses AI to automatically categorize expenses and transactions, taking the hassle out of bookkeeping. Plus, its intuitive interface makes accounting easy, even if you don’t have a financial background.


As your online business grows, Kashoo grows with you. It offers features to handle more complex accounting needs without needing to switch software. And it’s one of the most affordable options out there, perfect for startups and small businesses.


QuickBooks Online


QuickBooks Online has been a game-changer in cloud-based accounting since its launch in 2001. Trusted by millions of small businesses in over 190 countries, it offers a user-friendly interface that makes managing finances a breeze. Plus, it integrates with over 650 apps, so you can connect it with all your favorite tools.


One of the coolest features is the Live Bookkeeping service, where you can team up with certified QuickBooks ProAdvisors for expert help. There's also a special version for freelancers and self-employed pros, making it super easy to track your income, expenses, and taxes.


What really sets QuickBooks Online apart is its automation. The advanced AI handles transaction categorization and fraud detection for you. It even uses blockchain technology to keep your data secure and accurate.




This award-winning software might just solve your accounting headaches. Like Kashoo, KashFlow is designed to be user-friendly, even if you don't have a financial background. They’ve stripped away all the accounting jargon to keep things simple and straightforward.


KashFlow automates routine tasks like invoicing, bank reconciliation, and VAT returns, saving you time and reducing errors. Plus, with their mobile app, you can manage your finances on the go, handling invoicing, expense tracking, and getting real-time financial updates.


Being a UK-based company, KashFlow is fully compliant with GDPR, so your data is always secure. Still not convinced? Why not give it a try for free? KashFlow offers a trial period so you can explore all its features and benefits before making a commitment.




Here's another award-winning software you should check out: Xero. It's known for its impressive user experience. Not only does it offer beautifully designed, customizable financial reports and user-friendly dashboards, but it also comes with a mobile app that handles complex tasks like sending invoices and reconciling bank transactions.


With over 3 million subscribers in more than 180 countries, Xero is one of the most trusted accounting software options available. Unlike many others, Xero allows unlimited users at no extra cost, making it perfect for growing businesses like yours.


Xero connects to over 800 banks worldwide, making bank reconciliation and real-time financial tracking seamless. Plus, it has integrated payroll functionality, simplifying employee payments and compliance.




Back in 2003, Mike McDerment accidentally saved over an invoice, which inspired him to create software to prevent such mistakes. That software turned into FreshBooks.


Today, FreshBooks is a favorite for over 30 million users in more than 160 countries, making it a top choice for small businesses worldwide. Like KashFlow and Xero, FreshBooks has won numerous awards, especially for its exceptional customer service. It’s one of the few that offers 24/7 support via phone, email, and live chat.


What sets FreshBooks apart is its built-in time tracking, making it a breeze to log hours and bill clients. You can also snap photos of receipts to track expenses on the spot. And the cherry on top? FreshBooks includes project management tools for team collaboration, setting milestones, and tracking project progress.




Software subscriptions can be expensive, but not Wave. This software offers its core features for free, making it perfect for startups and small businesses looking to manage their finances without spending a fortune.


With Wave, you can create and send unlimited invoices at no extra charge. Its user-friendly design and smooth integrations make it easy to import transactions from your bank accounts and credit cards. Plus, you can customize invoices with your logo and brand colors for that professional touch.


Wave does more than just accounting; it also includes invoicing and receipt scanning, giving you an all-in-one financial management solution. It even offers payroll services with automatic tax calculations and filings, direct deposits, and employee self-service portals.


Sage Business Cloud Accounting


Sage has been a trusted name in accounting software since 1981, making it one of the oldest and most reliable players in the market. It quickly embraced cloud technology, so you can manage your finances efficiently without needing an in-house database.


For online sellers, having a clear view of your future financial position is crucial. Sage's advanced cash flow forecasting tools make this easy. Plus, its robust inventory management system tracks stock levels, manages product info, and sets reorder points effortlessly.


Sage allows multiple users to access the system with different permissions and roles, ensuring your team members only see and use what they need.


NetSuite ERP



NetSuite ERP is the perfect accounting software for your online store, and here’s why. First off, it’s an all-in-one suite that covers ERP, CRM, HR, and eCommerce. This means you can manage all your key processes with one system—no more juggling multiple software programs.


With NetSuite ERP’s real-time dashboards and reporting, you get instant insights into your performance, helping you make quicker decisions. Plus, as your business grows, there’s no need to switch to a new system because NetSuite ERP is designed to scale with businesses of all sizes.


Not only is it scalable, but it’s also incredibly flexible. You can customize and extend it to suit your specific needs. Whether it’s creating custom applications, workflows, or integrations, NetSuite ERP helps you streamline your processes and eliminate redundancy.




Just like NetSuite ERP, OneUp combines inventory management, CRM, and invoicing into one handy platform. It’s designed to make your life easier with features like automatic bookkeeping, so you can skip the hassle of manually matching your bank transactions to your invoices and expenses.


OneUp is great for real-time inventory tracking, perfect for businesses that need to keep a close eye on stock levels. If you work with international clients, you'll love that OneUp supports multiple currencies and tax systems, making global transactions a breeze.


Want to keep tabs on your financial health? OneUp generates detailed financial reports like profit and loss statements, balance sheets, and cash flow statements. And the best part? You can access these reports anytime, anywhere with their mobile app, available on both iOS and Android.


Time to Organize Those Numbers and Scale Up Your Online Biz!


Choosing the right accounting software can make or break your business. Pick the wrong one, and you might find yourself struggling.


When selecting accounting software, think about the tasks you need it to handle. Consider the type, complexity, and volume of your financial transactions. Look at both upfront costs and ongoing subscription fees. Ensure the software can grow with your business, handling more transactions and offering additional features as your needs change.


Don't forget to check out the provider. If you've never heard of them, their product might not live up to the hype. Go for software from a reputable vendor known for reliability, regular updates, and ongoing development. Doing your homework now can save you headaches down the road and help you find software you can rely on for years.