Running an e-commerce business can feel like a whirlwind—new orders, product listings, shipping, customer messages… and then there’s bookkeeping. While it may not be the flashiest part of online business, bookkeeping is absolutely essential to your success.
But e-commerce bookkeeping comes with its own unique set of challenges. Let’s explore a few of the most common ones—and what you can do about them.
1. Multiple Sales Channels = Multiple Headaches
Whether you’re selling on Shopify, Etsy, eBay, or all of the above, each platform has its own way of reporting income, fees, and refunds. Trying to reconcile everything manually is enough to make your head spin.
Tip: Use software that integrates with your sales channels and pulls everything into one place—or work with a bookkeeper who knows the ropes of e-commerce platforms.
2. Complex Fee Structures
Between platform fees, transaction fees, shipping costs, discounts, and returns, it can be hard to figure out what you actually earned from a sale. Your Stripe payout isn’t your revenue—it’s revenue minus all the fees.
Tip: Always record gross sales and break out fees separately. That way, you get an accurate picture of your real income (and can claim all your deductions at tax time!).
3. Inventory Accounting is Tricky
Unlike service businesses, e-commerce businesses have to track inventory costs. If you sell 100 mugs, but only track the sale price, you’re missing a key part of your profit equation: how much you paid for those mugs.
Tip: Implement a system to track inventory purchases, cost of goods sold (COGS), and stock levels. It doesn’t have to be fancy—but it does need to exist.
4. Sales Tax Confusion
Sales tax in e-commerce is… complicated. Depending on where your customers are, you may be responsible for collecting and remitting tax in multiple states or countries.
Tip: Use a tool like TaxJar or get advice from a tax professional. Don’t wait until your sales skyrocket—sales tax issues get more complex (and riskier) as you grow.
5. Cash Flow Surprises
Because payouts from platforms like Shopify and PayPal are delayed and fees are deducted first, your actual cash flow can be inconsistent and confusing.
Tip: Set up a cash flow tracker and always plan ahead for delays in receiving funds. It’s also smart to keep a cash reserve for slow periods or unexpected expenses.
Final Thoughts
E-commerce bookkeeping isn’t impossible—but it is different. The good news? Once you understand the challenges, you can plan for them—and avoid nasty surprises later.
If you’re feeling overwhelmed, you’re not alone. Plenty of successful online sellers struggle with the numbers behind their sales. But with a bit of support and the right systems, you can take control of your finances—and make confident, informed decisions for your business.
