Bookkeeping for Amazon + Shopify Sellers: What to Track (and What to Automate)
Running an eCommerce store on Amazon or Shopify means dealing with a flood of daily transactions, sales taxes, refunds, payouts, fees – and that’s just before lunch.
Download Our Free Brochure →If you’re trying to manage bookkeeping manually (or not at all), you’re risking messy records, inaccurate reports, and surprise tax bills. That’s why eCommerce brands – from solo sellers to scaling DTC companies – are turning to automated, CPA-reviewed bookkeeping with RemoteBooksOnline. Here’s what eCommerce businesses really need to track, what you can safely automate, and how we make it all easier.
What Makes Amazon + Shopify Bookkeeping So Complex?
Unlike service-based businesses, online sellers deal with:
- Multiple daily deposits from various channels
- Marketplace fees, refunds, and chargebacks
- Sales tax by state, city, and sometimes product type
- Inventory and COGS tracking
- Third-party app integrations for shipping, returns, discounts, etc.
Without structured books, you can’t see true profitability – or prep clean financials for tax season, investor meetings, or scaling decisions.
What You Need to Track (That Software Alone Can’t Handle)
| Area | Why It Matters |
|---|---|
| Gross vs. Net Sales | Needed for sales tax and growth visibility |
| Sales Tax Liabilities | Many states require detailed reporting |
| Marketplace Fees | Amazon, Shopify, PayPal, Stripe deductions |
| Cost of Goods Sold (COGS) | Direct impact on gross margin |
| Refunds and Returns | Affects both sales and COGS |
| Payout Timing | Delays between sale and actual deposit |
Tools like QuickBooks or Xero are great – but only when someone configures them properly, maps data sources, and reconciles accounts consistently.
What You Can (and Should) Automate
At RemoteBooksOnline, we help automate:
- Importing Amazon/Shopify payouts and mapping them to the right accounts
- Categorizing fees, discounts, and taxes using marketplace rules
- Reconciling accounts using your connected bank feeds
- Generating CPA-reviewed monthly financial reports
- Flagging anomalies (e.g., sudden refund spikes)
We make automation work for your business – not as a black box.
Test Case: 2-Product Shopify Brand Scaling to $250K/mo
A lifestyle brand selling home decor built their store on Shopify and handled all bookkeeping internally with spreadsheets. But once they hit $50K/month in sales, it became impossible to keep up.
RemoteBooksOnline stepped in:
Download Our Free Brochure →- Connected their Shopify store + Stripe accounts
- Automated payout reconciliation
- Categorized all expenses, refunds, and fees
- Delivered monthly financials reviewed by a CPA
Outcome: The founder stopped spending 10+ hours/month on books and used our reports to secure $150K in funding.
FAQs
Can you track Amazon and Shopify at the same time?
Yes. We support multichannel sellers – Amazon, Shopify, Etsy, Walmart, WooCommerce, and more.
Do I need QuickBooks or Xero?
We can work with either, and help you set up or optimize your system if needed.
Do you track COGS and inventory?
Yes. We use purchase history and inventory data to estimate and reconcile COGS monthly.
Will I get a P&L each month?
Yes. We provide CPA-reviewed P&L, balance sheet, and cash flow reports – every month.
Do you handle sales tax filing?
No – but we track what you owe by state so your sales tax service or CPA can file easily.
Selling on Shopify, Amazon, or Etsy? Our e-commerce bookkeeping services help you stay on top of inventory and revenue.
If you’re behind on your books, our catch-up bookkeeping services can help you get current fast-no stress, no mess.
Stay organized and tax-ready year-round with our flat-rate monthly bookkeeping services.
Your Sales Are Automated. Your Bookkeeping Should Be Too.
Stop guessing your profits and reconciling manually. Let RemoteBooksOnline give you CPA-reviewed clarity – without lifting a finger.
