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E-Commerce Bookkeeping

Bookkeeping Built for Online Sellers

Shopify, Amazon FBA, WooCommerce — we reconcile your payouts, track inventory costs, and keep your books clean across every channel.

Now with AI payout matching and channel margin tracking
The Problem

E-Commerce Accounting Is Genuinely Complex

Payout reports from Amazon and Shopify aren't actual income — they're net of fees, refunds, and reserves. Most bookkeepers get this wrong and overstate your revenue, creating tax problems down the line.

We understand how Shopify payouts work, how Amazon FBA fees affect COGS, how sales tax nexus functions across states, and how to reconcile multi-channel selling into one clean set of books.

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Shopify ReconciliationPayout-to-bank reconciliation, fee separation, refund handling
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Amazon FBA BookkeepingFBA fee tracking, inventory COGS, reimbursement recording
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Sales Tax ReportingMulti-state sales tax tracking and reporting for your CPA
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A2X & Synder IntegrationAutomated data feeds to QuickBooks or Xero — no manual entry

Platforms We Support

✓ Shopify
✓ Amazon FBA & FBM
✓ WooCommerce
✓ Etsy
✓ eBay
✓ TikTok Shop
✓ A2X Integration
✓ Synder Integration
Get Free E-Commerce Assessment →
What's Included

Complete E-Commerce Bookkeeping Service

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Monthly Reconciliation

Every payout, every platform, every month — reconciled to your bank statements accurately.

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COGS & Inventory Tracking

Know your true product costs and gross margins. Essential for pricing and profitability decisions.

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Sales Tax Setup & Tracking

Multi-state sales tax tracking with reports ready for your CPA at tax season.

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Monthly P&L Reports

Clean monthly profit and loss statements broken down by channel — so you know what's actually working.

AI inside this service

AI that untangles payouts, fees and inventory across every channel

E-commerce books break in the gap between a sale and the deposit that finally lands. Our AI layer reconciles Shopify, Amazon and Stripe settlements line by line, splits out fees and refunds, and watches your margins per channel — with a specialist accountant checking the edge cases.

  • Payout reconciliationEach settlement is matched back to orders, fees, refunds, chargebacks and reserves — so the bank deposit always ties to revenue.
  • Channel-level margin trackingGross margin by marketplace, product line and SKU family, updated as payouts clear rather than at quarter end.
  • COGS and inventory anomaly alertsSudden landed-cost swings, negative inventory and fee-rate changes are flagged before they distort your numbers.
  • Sales-tax nexus watchYour sales by state and country are monitored against economic-nexus thresholds, with a heads-up when you are approaching one.
Request an AI demo How AI fits into our bookkeeping
Maple & Co. — payout reconciliation Settlement 2 Feb

Amazon settlement #A-88213 fully matched1,204 orders · $41,318 net of $6,904 fees

Tied

Shopify payout matched to 312 ordersIncludes 9 refunds and 2 chargebacks

Tied

Amazon FBA fee rate up 1.8% vs JanuaryStorage fees on 3 oversized SKUs

+$412

Texas sales approaching $500k nexus threshold$462k trailing 12 months

92%
Accountant note: Storage fee driver confirmed; recommend clearing slow SKUs. Texas registration flagged to your CPA.
Common Questions

Frequently Asked Questions

Answers to the questions US business owners ask us most often about this service.

What is the best bookkeeping software for Shopify sellers?
QuickBooks Online paired with A2X is the most widely used and most effective combination for Shopify sellers. A2X automatically imports your Shopify payout data into QBO with the correct breakdown of gross sales, fees, refunds, and taxes — eliminating hours of manual entry. Xero with A2X is equally effective for sellers who prefer Xero's interface. Wave is a free option suitable for very low-volume sellers but lacks the integration depth of QBO or Xero.
How should I record Shopify payouts in QuickBooks?
Shopify payouts should not be recorded directly as income. The correct approach is: 1) Record gross sales as income using A2X or from your Shopify settlement report, 2) Record Shopify transaction fees and payment processing fees as separate expenses, 3) Record refunds as a reduction in revenue, 4) The net payout that hits your bank clears through a Shopify clearing account. The balance in the clearing account should match exactly to the bank deposit. Recording the payout directly as income overstates your revenue by the amount of fees paid.
Do Amazon FBA sellers need to file sales tax?
In most US states, Amazon acts as a marketplace facilitator and collects and remits sales tax on your behalf — so you do not need to register or file in those states for your Amazon sales. However, you should confirm which states Amazon covers for your account (found in Seller Central under Tax Settings) and determine if you have nexus through any other channel (your own website, other marketplaces) that would create an obligation Amazon does not cover.
What is the cost of goods sold (COGS) for an e-commerce business?
For an e-commerce business, COGS includes the cost of the products sold, inbound shipping to fulfilment centres or your warehouse, and packaging costs. It does not include platform fees, advertising, or fulfilment fees (which are selling expenses). COGS is matched to revenue in the period when the product sells, not when you purchase inventory. Tracking COGS accurately is essential for understanding your gross margin — the single most important profitability metric for a product business.
How do I handle multi-currency transactions in ecommerce bookkeeping?
Multi-currency bookkeeping requires your accounting software to support multiple currencies (both QBO Plus and Xero Premium do). Each transaction is recorded in the original currency and converted to your home currency at the exchange rate on the transaction date. At month-end, open foreign currency balances are revalued to the current exchange rate, generating unrealised gains or losses. A2X handles multi-currency Shopify transactions automatically for sellers using QBO or Xero.
What bookkeeping records do I need for an ecommerce business audit?
For an IRS audit or state sales tax audit, you need: bank statements for all business accounts, your full general ledger and transaction history in your accounting software, Shopify or Amazon settlement reports for each period, purchase invoices for all inventory purchased, receipts for all operating expenses, and sales tax return filings. Cloud accounting software like QBO and Xero makes this straightforward — everything is stored digitally and can be exported on demand.
How often should an ecommerce business reconcile accounts?
Monthly reconciliation is the standard. For high-volume sellers (over 1,000 transactions per month), bi-weekly reconciliation aligned with Shopify or Amazon payout cycles is cleaner and makes month-end faster. Weekly reconciliation is rarely necessary unless you are managing cash flow very tightly or your business has unusually complex multi-channel transactions. The key is consistency — reconciling once a month, every month, produces far better results than sporadic catch-up sessions.

Stop Guessing at Your E-Commerce Numbers

Book a free assessment and we'll show you exactly how we'd clean up your books.

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