E-commerce Bookkeeping (2025): Amazon/Shopify Fees, Payouts, COGS & Sales Tax
Marketplaces batch orders, refunds, chargebacks, fees, and reserves into lump-sum deposits. If you post only bank activity, revenue, COGS, and fees all go sideways. Our flow maps order-level detail → settlement summaries → GL so every deposit ties out.
Core workflow
- Data capture: Connect Amazon/Shopify/Etsy + gateways (Shopify Payments/PayPal/Stripe).
- Mapping: A2X/Webgility (or native exports) → chart of accounts (sales, discounts, refunds, gift cards, fees, reserves).
- Payouts: Each settlement reconciles to the bank; undeposited funds cleared.
- Returns/chargebacks: Posted to proper contra accounts; inventory adjusted when applicable.
- Inventory & COGS (FIFO): Landed cost (freight/duties) rolled into item cost; monthly inventory roll-forward.
- Sales tax: Nexus review; marketplace facilitator rules; state filings from reconciled sales.
- Month-end close: P&L by channel/SKU, cash flow, inventory and fee analytics.
Where Gen-AI helps (safely)
- OCR vendor invoices and shipping bills to capture landed cost.
- Anomaly flags for out-of-pattern fees, return spikes, or reserve changes.
- LLM draft notes for close package variances (human-verified; no customer PII sent to models).
Pricing guide (typical)
- Single-store, low volume: $500-$900/mo
- Multi-channel (Amazon + Shopify/Etsy), moderate volume: $900-$1,800+/mo
- High volume / multi-currency / 3PL: $1,800-$3,000+/mo
Deliverables you should expect
- Financials by channel and optionally by SKU/category
- Inventory roll-forward (beg + purchases – COGS – shrink = end)
- Fee analysis by marketplace and gateway
- Sales tax summary by state (marketplace vs. seller-collected)
- Exception log of AI-flagged items and resolutions
Tech stack we support
QuickBooks Online or Xero; A2X/Webgility; major gateways; bill pay & expense apps; 3PL exports; dashboards.
Want deposits that tie out and margins that make sense? Start your e-commerce close.
FAQs
How do you reconcile Amazon and Shopify payouts?
We map settlement detail (sales, discounts, refunds, fees, reserves) to the GL, then match each settlement to the bank deposit and clear undeposited funds. Every deposit ties to source data.
Can you track landed cost and FIFO COGS?
Yes. We OCR vendor invoices and freight/duties, roll them into item cost, and post FIFO COGS with an inventory roll-forward each month.
Do you handle multi-state sales tax?
We summarize marketplace-collected vs. seller-collected tax, monitor nexus thresholds, and prepare state filings based on reconciled sales.
What affects the monthly price the most?
Order volume, number of channels/gateways, inventory complexity, multi-currency, and sales-tax footprint.
Related Reading:
- Atlanta Bookkeeping Services: Cost, Duties & Packages (2025)
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