The Complete Guide to Ecommerce Bookkeeping in 2025 (Shopify, Amazon, TikTok Shop)

Why Ecommerce Bookkeeping Is Different

If you're managing your ecommerce finances like a traditional service business, you're almost certainly making costly mistakes. Ecommerce bookkeeping has unique challenges that most general accountants don't understand:

• Revenue arrives from multiple payment processors and platforms simultaneously
• Platform fees, advertising costs, and refunds are netted from payouts — not paid separately
• Inventory must be tracked and valued — and COGS calculated correctly
• Multi-currency transactions create exchange rate gains and losses
• Sales tax obligations vary by state, country, and platform

Shopify Bookkeeping: What You Need to Track

Revenue Reconciliation

Shopify pays out net — meaning platform fees, refunds, and chargebacks are already deducted from what hits your bank account. Your books need to record gross revenue, then deduct each cost separately. This is essential for accurate P&L reporting and tax compliance.

Cost of Goods Sold (COGS)

Every product sold has a cost — the price you paid your supplier, plus shipping and import duties. Your bookkeeping system must track and record this cost whenever a sale is made, not when you buy inventory. This is called the matching principle.

Multi-Currency

If you sell in GBP, USD, AED and EUR simultaneously, your books need to record every transaction in your functional currency and recognise exchange rate differences. Most Shopify sellers overlook this — and end up with inaccurate profit figures.

We connect your Shopify store directly to QuickBooks Online — automating the reconciliation of revenue, fees, refunds, and payouts every month.

Amazon FBA Bookkeeping: The Unique Challenges

FBA Fees

Amazon deducts fulfilment fees, storage fees, referral fees, and advertising costs from your payouts. These must be separated and categorised correctly in your books — not lumped together as "Amazon fees".

Inventory at Amazon Warehouses

Inventory sent to Amazon but not yet sold is still an asset on your balance sheet. Your bookkeeping system must track this separately from inventory already sold. Many Amazon sellers dramatically understate their assets by ignoring this.

Reimbursements

Amazon regularly reimburses sellers for lost or damaged inventory. These reimbursements are income — and must be recorded correctly to avoid understating your revenue.

TikTok Shop Bookkeeping

TikTok Shop is newer but growing rapidly. The bookkeeping challenges mirror Shopify and Amazon — platform fees, creator commissions, affiliate payouts, and advertising costs all need separating from gross revenue. Monthly reconciliation of your TikTok Shop dashboard to your bank account is essential.

The Right Accounting Software for Ecommerce

QuickBooks Online integrates natively with Shopify, Amazon, TikTok Shop, and most payment processors. It automates the import of transactions, categorises fees, and produces monthly P&L reports you can actually rely on.

Xero is another excellent option, particularly for UK and Australian ecommerce sellers. Its bank feed reconciliation is fast, accurate, and handles multi-currency well.

Both platforms allow your accountant to access your books remotely — meaning your outsourced ecommerce bookkeeper can keep your records up to date without ever needing to visit your office.

How Often Should You Do Ecommerce Bookkeeping?

Monthly, at minimum. Weekly is better for high-volume stores. Leaving bookkeeping to once a year (at tax time) creates months of errors to untangle and means you're making business decisions — on pricing, advertising spend, and inventory — without accurate financial data.