Bookkeeping for e-commerce looks simple from the outside. Money in, money out—right?
Not quite.
Once you throw in inventory, merchant fees, returns, sales tax across states, and syncing Shopify with QuickBooks... chaos. Most e-commerce founders come to Sam’s List when they’ve tried to DIY for too long and it’s finally caught up to them.
Here’s what we see most often—and how to clean it up before it costs you time, money, or worse: tax penalties.
Looking for abookkeeperfor your Ecommerce business? Check outSam's Listto find a list of accountants and bookkeepers that specialize in working with Ecommerce businesses!
| Mistake | Why It Matters |
| Not tracking cost of goods sold (COGS) | You’ll overestimate profit and pay too much tax |
| Ignoring platform fees | Shopify, Stripe, and Amazon all take a cut |
| Not reconciling payouts | Your books won't match your bank account |
| Using personal accounts for inventory | Messy records, hard to track what’s deductible |
| Delaying cleanup until tax season | Leads to panic, overpayment, or missed write-offs |
“E-commerce brands especially need help—inventory is no joke. Bad books don’t just hurt you during tax time. They can hide cash flow issues or hold you back from scaling.”
— Kimi, Co-founder ofSam’s List
| Category | Details You Need to Track |
| Revenue | Gross sales, returns, discounts by channel (Shopify, etc.) |
| COGS | Inventory purchases, freight, duties |
| Platform Fees | Shopify, Stripe, PayPal, Amazon, etc. |
| Advertising Spend | Meta, Google Ads, influencer payouts |
| Operating Expenses | Subscriptions, software, rent contractors |
| Sales Tax Liability | State-by-state, especially for nexus compliance |
| Net Profit + Cash Flow | Not just sales--what'sactuallyleft |
When to Stop Doing It Yourself
If you’re doing more than $20K/month in revenue, bookkeeping is no longer a side task—it’s a business risk if ignored.
“We’ve seen clients spending hours per week syncing Shopify to QuickBooks and still ending up with unreliable books. If you want to scale, outsource this.”
When to Hire an E-Commerce Bookkeeper
You sell onmultiple platforms(Shopify, Amazon, Etsy, etc.)
You useapps or toolsthat affect inventory, pricing, or fulfillment
You’re spending3+ hours/weekon books
You’ve crossed$250K in annual revenue
You’re planning tofundraise or take on a loan
👉 Find a Bookkeeper Who Specializes in E-Commerce
FAQ
How do I do bookkeeping for Shopify?
You’ll need to track gross revenue, fees, returns, shipping costs, and sync with your accounting software. Shopify alone doesn’t give you full financial visibility.
What’s the best bookkeeping software for e-commerce?
QuickBooks or Xero, paired with A2X, are solid options. Wave is fine for super small brands but doesn’t support inventory well.
Do I need an accountant for my e-commerce business?
Not always—but if you’re selling across states or using inventory, a bookkeeper or accountant can help you avoid tax and cash flow issues.
Can I use Excel for e-commerce bookkeeping?
Youcan… but it won’t scale. Once you hit 100+ monthly transactions, you’re better off with software or a professional.
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Author: Kimi, Co-founder of Sam’s List
Kimi writes about what she's learning while building Sam’s List and shares honest takeaways from her conversations with accountants and financial advisors across the country. None of this is financial advice—just the stuff most people wish someone told them sooner.
