Ecommerce Bookkeeping for Shopify, Amazon & Multi-Channel Sellers
Ecommerce bookkeeping that reconciles Shopify/Amazon payouts, maps fees/reserves, fixes inventory & COGS timing, and aligns sales tax. CPA-reviewed month-end in QuickBooks or Xero.
At a glance: Amazon/Shopify/Etsy bookkeeping • inventory & COGS (FIFO) • landed cost & freight • A2X/Webgility mapping • marketplace fee & payout reconciliation • returns/chargebacks • gift cards/store credit • sales tax nexus prep (works with Avalara/TaxJar/your CPA) • multi-channel & multi-currency • QuickBooks setup/cleanup • CPA-reviewed monthly close • flat-rate • first month free • nationwide
Ecommerce bookkeeping has to make margins real—every month. We run your books in QuickBooks or Xero with clean payout mapping (gross → fees → refunds/chargebacks → reserves = net deposit), correct inventory and COGS timing, and marketplace-facilitator sales-tax logic. We standardize SKU mapping, normalize gateways (Stripe/PayPal), and reconcile every payout to bank statements so your revenue, fees, reserves, refunds, and FX are accurate. Each month we reconcile all bank/credit/loan accounts, clear Undeposited Funds, tie AR/AP to the GL, and produce a CPA-reviewed reporting pack (P&L, Balance Sheet, AR/AP aging, cash highlights) with variance notes and a period-lock recommendation. Whether you sell on Shopify, Amazon, or a multi-channel stack, you’ll get channel-level margins you can trust—and lender-ready statements without manual patchwork.
Why Choose Us (ecommerce-specific value)
What’s Included (Scope of Work)
| Service | Description |
|---|---|
| Payout Mapping | Gross sales, fees, refunds, chargebacks, reserves → net deposit; channel-level tie-out. |
| Inventory & COGS | Item-level or periodic COGS; valuation tie to subledger/IMS; landed cost options. |
| Sales Tax | Marketplace-facilitator vs direct cart logic; liability true-up to returns. |
| Gateways | Stripe/PayPal fee mapping and reconciliation to statements. |
| Reconciliations | Bank/credit/loan accounts tied to statements; undeposited funds cleared to zero. |
| Adjusting Entries | Accruals, prepaids, FX revaluations; posted with workpapers. |
| Reporting Pack + CPA Review | P&L (by channel/class), Balance Sheet, AR/AP aging, cash highlights, variance notes, period-lock guidance. |
Process (Simple, reliable, and built for speed)
Assess & Scope
15-minute fit call, read-only statements, channel/gateway review.
Cleanup & Onboard
SKU mapping, payout rules, historical fixes (if needed).
Run
Weekly imports, payout tie-outs, month-end reconciliation and reporting.
CPA Review
Reconciliations, adjustments, variance notes, period-lock recommendation.
Pricing
Note: Cleanup quoted separately by months of backlog.
Schedule Your Free E-commerce Bookkeeping Consultation Now!
Let RemoteBooksOnline manage your bookkeeping efficiently, freeing you to focus on growing your e-commerce business.
How Our Ecommerce Bookkeeping Works
Connect & Scope
We connect Amazon, Shopify, Etsy, gateways (Shopify Payments/PayPal) and choose A2X/Webgility where useful.
Map & Configure
Chart of accounts for inventory/COGS (FIFO), sales channels, taxes, discounts, gift cards, and fees.
Code & Reconcile
Import settlements, post fees, match payouts, clear undeposited funds, reconcile bank & cards monthly.
Close & Report
CPA-reviewed close: P&L by channel/SKU, cash flow, inventory roll-forward, sales tax summaries, tax-ready.
Client Reviews
We support business owners across the country with reliable, remote bookkeeping. Here’s what a few of them say:
RemoteBooksOnline dramatically simplified bookkeeping for my Shopify store. Highly recommended!
Emma W, Shopify Store Owner
The integration with our Amazon and Shopify stores was seamless. Perfect service for us.
Alex D, Multi-Channel Seller
I spend less time worrying about my books and more time growing my Shopify business.
Olivia B, E-commerce Seller
Frequently Asked Questions
Yes, we seamlessly integrate with major platforms like Shopify, Amazon, and Etsy.
Yes. Returns/chargebacks, discount codes, gift cards, and store credit are categorized so margins remain accurate.
Yes, we specialize in bookkeeping services tailored specifically for Shopify sellers.
No special software is required. We handle everything remotely using secure, cloud-based platforms.
Yes—reserves and releases are separate lines; chargebacks and refunds are mapped to the proper contra revenue/expense accounts.
We align SKU mapping and choose item-level or periodic COGS, then reconcile valuation to the subledger/IMS and sales timing.
Onboarding in 3–7 business days; cleanup (if needed) completes in 1–4 weeks.
Yes, we accurately track and reconcile Etsy marketplace fees for online sellers.
Absolutely, we offer competitively priced packages perfect for small and medium-sized e-commerce businesses.
Absolutely. We consolidate sales, refunds, and fees from multiple channels including Stripe, PayPal, Amazon, and more, all into one clean set of books.
See more in our full E-Commerce Bookkeeping FAQ →
Schedule Your Free E-commerce Bookkeeping Consultation Now!
Let RemoteBooksOnline manage your bookkeeping efficiently, freeing you to focus on growing your e-commerce business.
Featured Insights
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Helpful Articles for E-commerce Bookkeeping
Want to understand how bookkeeping works for Amazon, Shopify, and other platforms? These blog posts break it down:
6 Bookkeeping Tips Every E-commerce Seller Should Know
- Managing Inventory and Financials for Shopify and Amazon Sellers
- Remote Bookkeeping vs. Local Bookkeepers: What’s Best for Your Business?
- The Real Cost of DIY Bookkeeping for Small Business Owners
- What Services Are Included in Professional Bookkeeping?
Which Bookkeeping Service Do You Need?
Each page provides detailed information on how we help solve specific pain points-whether you're behind on your books or looking to fully outsource.