The bank deposit is not the sale
An ecommerce platform may collect customer revenue, sales tax, shipping, tips, or other amounts, then subtract refunds, chargebacks, platform fees, payment fees, reserves, and adjustments before sending a net deposit to the bank. Recording that net deposit as revenue compresses several economically different events into one number.
The bookkeeping system should preserve gross sales and the deductions that explain how gross activity became net cash. That is what makes channel margins, tax records, and processor reconciliation usable.
Build a settlement reconciliation
For each major platform or processor, maintain a clearing account. Sales and other customer activity increase the clearing balance; refunds, fees, disputes, and transfers reduce it; payouts clear the balance to cash. At period-end, the remaining balance should be explainable by unsettled transactions, reserves, or timing differences.
This is especially important when several stores or processors pay into the same bank account. The bank alone cannot tell you which channel generated the activity.
Keep sales tax separate from revenue
Amounts collected from customers for sales tax generally need to be tracked separately from operating revenue. Marketplace-facilitator rules, registration requirements, and filing responsibilities vary by state and channel, so the accounting should preserve enough detail for the tax process rather than assuming every tax collected belongs to the business.
The bookkeeping team should reconcile sales-tax liability accounts to filed returns or marketplace reports and flag states where transaction patterns suggest a registration review may be needed.
Inventory changes the close
A product business needs a repeatable way to move inventory purchases into cost of goods sold as products are sold. The exact method depends on the accounting and tax facts, but operationally the company needs reliable unit, landed-cost, write-off, return, and inventory-on-hand data.
If inventory is material, a bookkeeper should not simply expense every supplier payment. Doing so can distort gross margin and make one month look terrible because stock was purchased for future periods.
Returns, discounts, gift cards, and chargebacks deserve their own treatment
High-return businesses need visibility into returns rather than netting them silently against sales. Discounts can be tracked consistently so gross-to-net revenue is understandable. Gift cards and customer credits may create obligations until redeemed. Chargebacks should be separated from ordinary refunds because they can include dispute fees and processor-specific timing.
The goal is not to create dozens of accounts. It is to preserve the few categories that explain unit economics and cash conversion.
A useful ecommerce month-end package
- P&L with revenue and gross margin by meaningful channel where possible.
- Processor reconciliation from gross activity to payouts.
- Inventory balance and cost-of-goods-sold support.
- Refund, discount, and chargeback trend.
- Sales-tax liability and filing-status review.
- Advertising spend and contribution-margin view when management uses it.
- Cash and working-capital summary, including processor reserves or delayed payouts.
Design the books around how the store actually operates
A small Shopify store does not need enterprise accounting architecture. A multi-channel brand with Amazon, wholesale, subscriptions, several processors, inventory locations, and large ad spend does. Start with clean settlement reconciliation and add detail only when it supports a decision, a filing, or a control.
That approach keeps ecommerce bookkeeping understandable while still making the numbers strong enough for tax preparation, financing, and a future CFO or buyer.