Clicks, Carts, and Clean Books: 5 Bookkeeping Tips Every E-Commerce Store Needs to Know

Running an e-commerce store can feel like a whirlwind—between product sourcing, marketing, customer service, and shipping logistics, your “to-do” list is probably longer than your packing slips. But if there’s one thing you don’t want to leave behind in the chaos, it’s your bookkeeping.

Whether you’re selling handmade jewelry on Etsy or managing a full Shopify empire, keeping your financials in check is just as important as making those sales. Not only will it save you stress come tax time, but it’ll also help you understand how your biz is actually doing.

Young freelance Asian woman using laptop packing cardboard box in living room at home at night. Working from home concept.

Here are 5 simple-but-powerful bookkeeping tips to keep your e-commerce store profitable and panic-free:

1. Separate Your Business and Personal Finances (For Real)

We get it—it’s easy to swipe your personal card when you’re in a rush or just starting out. But mixing business and personal transactions is a recipe for confusion and CRA nightmares.

Do this instead:

Open a dedicated business bank account and credit card.
Run only business transactions through them.

Bonus: Your bookkeeper (or future you) will thank you.

Accounting journal and laptop. Hand on book for accounting. Keep bookkeeping.

2. Track Every Sale (Even the $2 Ones)

With orders flying in from multiple channels—Shopify, Amazon, Etsy, WooCommerce—it’s tempting to just look at your Stripe payout and call it a day. But you need to know where your revenue is coming from.

Pro tip: Use an integrated bookkeeping system (like QuickBooks Online) that connects to your sales platforms and auto-syncs your transactions.

That way:

You don’t miss a sale
You can see which products or channels are really making you money
Your gross vs net revenue is crystal clear

Asian business man startup SME entrepreneur or freelance working in a cardboard box prepares delivery box for customer, Online selling, e-commerce, packaging and shipping concept

3. Don’t Forget About Fees

Merchant fees, transaction fees, platform fees, shipping fees… they add up faster than you can say “abandoned cart.”

Make sure you’re recording:

Payment processor fees (Stripe, PayPal, Square)
Marketplace fees (Amazon, Etsy, etc.)
Shipping and fulfillment costs

Why it matters: You might be selling $50 items… but if $10 of that goes to fees, your profits aren’t what they seem.

asian online shop seller packing box for sending to customer buy goods from online store.e-commerce for start up small business concept

4. Stay on Top of Inventory and COGS

Cost of Goods Sold (COGS) is a major part of your financial story. If you're not tracking it, you're flying blind.

Get into the habit of:

Recording how much your products cost (including shipping & duties)
Updating inventory regularly
Using tools that sync inventory with your books

It’s not just about taxes—it’s about knowing your true margins and making smarter pricing decisions.

5. Review Your Numbers Monthly (No Ghosting Allowed)

Don’t wait until year-end to figure out if you made a profit. Set aside time each month to check in on your books.

Look at:

Your income statement (aka profit & loss)
Bank and credit card reconciliations
Cash flow (what’s coming in vs. going out)

If things aren’t adding up, catch it now—not when your accountant is chasing you during tax season.

Top view of young woman accountant doing tax audit

Final Thoughts

Bookkeeping isn’t just a boring backend task—it’s your store’s financial GPS. Whether you're planning to scale, prep for tax season, or just sleep better at night, clean books are the way to go.

If it still feels overwhelming, don’t worry—you don’t have to DIY forever. A good e-commerce-savvy bookkeeper can help you stay organized, tax-ready, and on track to grow.

Ready to go from spreadsheet stress to financial clarity? We’re here for that.