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.
Where Ecommerce Bookkeeping Fits in Your Online Store Workflow Ecommerce stores depend on clean sales, refunds, COGS, payment gateways, and inventory tracking:
- Clean up or catch up past sales, refunds, fees, and deposits
- Reconcile merchant processors and marketplace payouts
- Track inventory, shipping, COGS, discounts, and returns
- Add accounting, tax, and outsourced support as order volume increases
If your books are behind, begin with QuickBooks Cleanup or Catch-Up Bookkeeping. Once aligned, Monthly Ecommerce Bookkeeping and Accounting Services keep reports accurate.
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:
Outstanding security measures make me confident in your bookkeeping services.
Mark T, Small Business Owner
Accurate inventory bookkeeping has improved our profitability. Great team!
Jessica L, Inventory Manager
Fast onboarding and excellent service for my new e-commerce business.
Steven K, Online Retailer
Frequently Asked Questions
Yes. Returns/chargebacks, discount codes, gift cards, and store credit are categorized so margins remain accurate.
Yes, we accurately track and reconcile Etsy marketplace fees for online sellers.
Yes—reserves and releases are separate lines; chargebacks and refunds are mapped to the proper contra revenue/expense accounts.
Yes, our monthly bookkeeping services are CPA-reviewed for accuracy and compliance.
We align SKU mapping and choose item-level or periodic COGS, then reconcile valuation to the subledger/IMS and sales timing.
QuickBooks Online and Xero.
A2X, Webgility, Synder, and custom integrations.
Standardized chart of accounts and monthly close checklist.
Yes, inventory tracking and cost-of-goods-sold management are core parts of our bookkeeping services.
Yes, we split sales, fees, refunds, and taxes for accurate COGS.
See more in our full E-Commerce Bookkeeping FAQ →
Which Bookkeeping path fits your Ecommerce Store?
Ecommerce brands manage orders, payouts, fees, refunds, and channels. Some are months behind, others just need a clean monthly close, and some want full accounting and cash-flow support.
Most ecommerce stores choose one of these paths:
If you’re behind or payouts don’t match:
If you want a clean monthly close:
If you need deeper accounting and cash-flow reporting:
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
Discover how our expert bookkeeping services tackle real business challenges
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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.
If you’d like quick explanations for ecommerce terms such as payouts, marketplace fees, inventory adjustments, or SKU-level accounting, you can review the Glossary for clear definitions and context.