Choosing the Best Accounting Software for Online Sellers: A Comparison Guide

Alright, so you're running your own online store, making sales, and seeing that money flow in. But then, the dreaded question pops up: "How do I keep track of all this?!" 😱 If you're looking to keep your books clean without the headache, you’re in the right place. Let’s talk accounting software—the lifeline of any e-commerce business, whether you’re selling handmade candles, cookies, tech gadgets, or any other else.

Don’t worry, we’re going to walk through this in a way that even your grandma could understand. So let’s dive in and explore the best accounting software for online sellers—and sprinkle in some humor along the way to make this less of a snooze fest.

What is Accounting Software and Why Do You Need It?

First things first, accounting software helps you track your sales, expenses, inventory, and taxes (hello, GST/VAT!) without you pulling out your hair. As your online store grows, it’s way too easy to lose track of those dollars and cents. Trust us, spreadsheets only take you so far before they become a chaotic mess. No one needs to be drowning in numbers.

Accounting software helps with:

• Invoicing (Say goodbye to writing invoices by hand!)
• Expense Tracking (Where did all your money go? It wasn’t the office coffee machine, was it?)
• Inventory Management (Did you sell out of your best-selling item? Your software will know before you do.)
• Tax Compliance (Yup, the IRS/BIR isn’t a fan of surprises).

Now, let’s get into the good stuff—a side-by-side showdown of the best accounting software for your online store.

Top Accounting Software for Online Sellers

Product	Best for	Starting at	Promotion	Learn More
QuickBooks Online	Overall best for e-commerce accounting	$9.50/month for the first 3 months then $19/month	👉 50% off for the first 3 months or a free 30-day trial	👉 Visit QuickBooks
Xero	Best for multiple users	$15/month Additional tiers: $47, $80	👉 30-day free trial or monthly discount (terms vary)	👉 Visit Xero
Zoho Books	Best value for e-commerce	$0 Additional tiers: $20, $50, $70, $150, $275	👉 14-day free trial of the Premium plan	👉 Visit Zoho Books
FreshBooks	Ideal for small service-based businesses	$19/month Additional tiers: $33, $60, custom	👉 30-day free trial or monthly discount	👉 Visit FreshBooks
A2X	Best for e-commerce marketplaces	$29/month Additional tiers: $79, $89	👉 Free trial (unlimited time with limited features)	👉 Visit A2X
QNE	Best for Philippine tax compliance	Contact for pricing Customized pricing plans available	👉 Free demo available upon request	👉 Visit QNE
Odoo	Best for comprehensive ERP integration	$25/month per user Additional apps may incur extra costs	👉 15-day free trial available	👉 Visit Odoo

1. QuickBooks Online: For the Big Dreamers

QuickBooks is the go-to solution for a lot of small business owners. It’s like the Swiss Army knife of accounting—minus the corkscrew (unless you need it, no judgment here).

Key Features:

• E-commerce Integrations: Shopify, Amazon, you name it. QuickBooks plays nice with your online shop.
• Invoicing: Easy to send and track.
• Inventory Management: Yes, it even helps you keep track of what’s on your shelves.
• Reports & Tax Tools: It’ll even help you with those scary tax forms.

Pros:

• Well-established, trusted by small businesses.
• Easy to use, even for people who break out in hives when hearing “accounting.”
• Decent customer support (because we all need someone to talk us off the ledge).

Cons:

• It's a bit on the pricier side.
• Inventory management? Only on the higher-tier plans, so don't expect it for pocket change.

Pricing: Starts at $25/month.

The Verdict: If you’re planning on growing your store (and maybe even your empire), QuickBooks is like a trusty sidekick who always knows what’s going on.

2. Xero: For the Collaborators and Scalability Seekers

If you’ve ever dreamed of running a business with a tight-knit team, Xero’s got your back. It’s built for collaboration—the more, the merrier. And if you want your accounting team to have an easier time doing their thing, Xero’s cloud-based features will make their day. It’s a little like a digital party for accountants.

Key Features:

• E-commerce Integrations: It works with platforms like WooCommerce, Shopify, and BigCommerce. Perfect for keeping your store running smoothly.
• Bank Feeds: Automatically imports transactions—because nobody wants to manually enter every penny.
• Multi-user Access: Multiple team members? No problem.

Pros:

• Super affordable for smaller businesses.
• Amazing for collaboration—your accountant and you will get along like peas in a pod.
• Solid reporting features to help you keep track of everything.

Cons:

• Inventory management? Not in the base plan. Sorry!
• The user interface can take a bit of getting used to.

Pricing: Starts at $13/month.

The Verdict: Xero’s ideal for businesses looking to start small and scale up. Just don’t expect full inventory management at the lower-tier plan.

3. FreshBooks: For the Invoicing Gurus and Simple Souls

FreshBooks is like your favorite cup of coffee—smooth, easy, and always there when you need it. It’s great if you’re a freelancer, small online seller, or anyone who needs an invoicing machine that gets the job done without any fuss. You won’t need a degree in accounting to use this.

Key Features:

• Invoicing: Automatically generate invoices for your customers. You can even send reminders when they’re late (in the nicest way possible, of course).
• Expense Tracking: Track what you’re spending with a simple receipt scanner.
• Time Tracking: For service-based online businesses, FreshBooks even helps you track how long you work on each project.

Pros:

• Simple and intuitive. You won’t need an accounting degree to use it.
• Great for freelancers and small businesses with straightforward needs.
• Excellent customer support that actually answers the phone.

Cons:

• Inventory management? Not in this tool.
• Lacks advanced features for growing e-commerce stores.

Pricing: Starts at $15/month.

The Verdict: FreshBooks is a winner for those who want an easy-to-use, no-nonsense accounting solution. But if your store is growing fast and requires inventory management, you might need to look elsewhere.

4. QNE Accounting: For the Philippine-Based Powerhouses

If you’re in the Philippines (or Southeast Asia), QNE Accounting is an excellent local option. It’s tailor-made for businesses that want to stay compliant with local tax laws (hello, VAT!) and is designed with the region in mind.

Key Features:

• Local Tax Compliance: Keeps you in line with Philippine tax regulations.
• E-commerce Integrations: Works with platforms like Shopify and Lazada.
• Inventory Management: Track your products and ensure you're not selling your last unit of that best-seller by accident.

Pros:

• Made for the Philippines—it’s like having a local expert on your side.
• Good inventory management and tax compliance features.
• Affordable pricing for local businesses.

Cons:

• Limited integration with global platforms.
• It’s more suitable for businesses in the Philippines, so if you're international, proceed with caution.

Pricing: Starts at ₱3,000/month.

The Verdict: Perfect for local businesses in the Philippines that need solid inventory tracking and tax compliance. It’s not the best for international sellers, though.

5. Odoo Accounting: For the All-in-One Solution Seekers

Odoo is like the Lego set of accounting—pick and choose what you need. It’s more than just accounting; it’s an entire business management platform. It can handle inventory, CRM, sales, and yes, accounting all under one roof.

Key Features:

• Customizable Modules: Add features as your business grows.
• Inventory Management: Excellent for keeping track of stock levels.
• E-commerce Integrations: WooCommerce, Shopify, and Magento are all supported.

Pros:

• Highly customizable—you can mix and match features as you need.
• Great for growing businesses—it scales with you.
• Comprehensive—it integrates all aspects of business management.

Cons:

• Can get expensive as you add more modules.
• Steeper learning curve compared to other options.

Pricing: Starts at $20/month.

The Verdict: Odoo is perfect for businesses that need everything in one place—from inventory management to accounting to CRM. Just be ready for a learning curve.

The Final Verdict:

If you’re just starting out with a small store and don’t need advanced inventory management, FreshBooks or Xero could be your best bet. However, if you’re looking for something more robust with inventory management, QuickBooks Online or Odoo will serve you well as your business grows.

And if you’re in the Philippines, QNE Accounting is a fantastic option to keep you compliant with local taxes and handle inventory all in one place.

So, grab your favorite accounting tool and get back to what you do best—selling amazing products and building your e-commerce empire! 😎