Nobody enjoys the busywork of ecommerce data entry, reconciliation and sales tax compliance. We integrate all your sales channels and give you one consolidated picture in QuickBooks, Xero or whichever accounting software you use.
Get accurate accounting and reconciliation across your stores, with sales flowing in automatically instead of being typed in by hand: platforms like Shopify, BigCommerce, Adobe Commerce (Magento) and WooCommerce, and marketplaces like Amazon, eBay and Etsy. Each payout is broken down into its parts: sales, refunds, taxes, shipping charges, discounts and fees.
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Ecommerce bookkeeping services we provide
- Integrating your stores and marketplaces with your accounting software
- Reconciling sales and payouts across every channel
- Knowing exactly what you pay in marketplace fees, payment processing and shipping
- Sales-tax nexus tracking across states and marketplaces
- Inventory and cost of goods sold, so your margins are real
- Seeing your whole multi-channel business in one set of reports
We close your books every month, typically by the 7th to 10th business day, so you see last month’s profit by channel while it can still change decisions on ad spend, pricing and reorders. We work in QuickBooks Online, Xero, NetSuite or whichever ledger you already use, and with settlement tools such as A2X that turn each payout into a clean summary entry.
Amazon seller bookkeeping
Amazon pays you a net deposit after taking referral fees, FBA fulfillment and storage fees, advertising, refunds and sometimes a reserve. Recording that deposit as sales understates both your revenue and your costs. We break every settlement into gross sales, each fee type, refunds, reimbursements and reserves, and reconcile it to the deposit in your bank, so your margin by channel is accurate.
- Settlement reports reconciled to bank deposits, period by period
- Referral, FBA, storage and advertising fees recorded as separate expenses
- Inventory held in Amazon warehouses tracked as your inventory, with cost of goods sold when it sells
- Marketplace facilitator sales tax separated from tax you collect yourself
Books behind after a busy season? We catch them up first with a fixed-fee cleanup and catch-up. To see where your sales may require sales tax registration, use our sales tax nexus checker.
Shopify bookkeeping
Shopify Payments deposits arrive net of processing fees, refunds and chargebacks, while app subscriptions and shipping labels are billed separately. We record gross sales, discounts, shipping income, sales tax and each fee type, then reconcile every payout to your bank, so revenue, margin and the sales tax you owe are all correct.
- Shopify Payments, PayPal and other gateway payouts reconciled to bank deposits
- Gross sales, discounts, refunds and shipping income recorded separately
- Sales tax collected tracked by state, ready for your filings
- Inventory and cost of goods sold, including 3PL and fulfillment costs
How should an ecommerce business account for inventory?
Inventory you buy is an asset until it sells; only then does it become cost of goods sold. Expensing every purchase order as it is paid makes a month with a big restock look like a loss and a month of heavy sales look too profitable. We track inventory on the balance sheet and record cost of goods sold as units sell, including the landed cost: the product, inbound freight, duties and tariffs, and prep or 3PL receiving fees.
- Inventory value tied out to your inventory system or Amazon and 3PL reports every month
- Landed cost per unit, so tariffs and freight show up in your margin
- Shrinkage, damaged and removed units written off when they happen
- Year-end inventory numbers ready for your tax CPA
How does sales tax work for online sellers?
Every state with a sales tax has a marketplace facilitator law, so Amazon, Etsy, eBay and Walmart collect and remit the tax on sales made through them. Sales on your own Shopify or WooCommerce store are your responsibility once you have nexus in a state, which usually starts at $100,000 of sales into that state, or $500,000 in states such as California, New York and Texas. Marketplace sales can still count toward those thresholds in many states. Our sales tax nexus checker shows every state’s threshold, and we keep the sales tax you collect in a liability account so it never gets counted as revenue.
Which numbers should an ecommerce owner review each month?
- Gross margin by channel, after marketplace fees, payment processing and fulfillment
- Advertising spend as a share of sales, by channel
- Refunds and chargebacks as a share of sales
- Inventory on hand and weeks of cover, so cash isn’t tied up in slow stock
- Cash, payouts in transit and Amazon reserves, so you know what you can actually spend
Monthly bookkeeping starts at $199 a month for very small stores; multi-channel sellers with inventory are quoted on volume after a free consultation. See pricing, and our guide to Black Friday bookkeeping for Shopify and Amazon sellers for the busiest weeks of the year.
Frequently asked questions
Which ecommerce platforms do you work with?
Shopify, BigCommerce, Adobe Commerce (Magento) and WooCommerce stores, and marketplaces including Amazon, eBay and Etsy, including sellers who use several channels at once.
Can you reconcile Amazon and Shopify payouts?
Yes. Payouts arrive net of fees, refunds and reserves, so we reconcile each payout back to the underlying sales and record fees, refunds and shipping separately. That’s how you see your real margins.
Do you help with sales tax for online sellers?
Yes. We help you understand where you have sales tax obligations, connect your sales data to your accounting software, and keep sales tax collected reconciled by state, ready for whoever files your returns, including for international sellers.
Should I record Amazon deposits as sales?
No. A deposit is what is left after Amazon takes its fees, refunds and reserves. Recording it as sales understates both revenue and costs, so we record gross sales and each fee separately and reconcile the total to the deposit.
What is A2X and do I need it?
A2X is a tool that turns each Shopify, Amazon or other marketplace payout into a summarized journal entry with sales, fees, refunds and taxes split out. It is not required, but for sellers with many orders it makes reconciliation faster and more accurate, and we work with it and similar tools.
Do I need accrual accounting for my online store?
Once you hold inventory or sell on several channels, accrual accounting gives a far truer picture of monthly profit, because inventory is expensed when it sells rather than when you pay for it. Very small sellers can start on a simpler basis and switch as they grow.
Will I get a Form 1099-K from Shopify, Amazon or PayPal?
Payment platforms and marketplaces issue Form 1099-K when your payments pass the federal reporting threshold, which is $20,000 and 200 transactions again after the One Big Beautiful Bill Act reversed the lower thresholds. Some states use lower thresholds. Your books should reconcile to the gross amount on the form, before fees and refunds.
How do you handle tariffs and import duties?
They are part of the cost of your inventory. We add duties, tariffs and inbound freight to the landed cost of each shipment, so they flow into cost of goods sold as the units sell and show up in your real margin.
How soon after month-end are my books closed?
Typically by the 7th to 10th business day of the following month, once payouts, settlement reports and bank statements are in.
Do you file sales tax returns?
We keep your sales tax records accurate and reconciled by state and work alongside the sales tax software or advisor you use for filings. For many sellers, a service such as Avalara or TaxJar handles the actual returns.
Get one clear picture of your store
Sound advice and bookkeeping support to keep your ecommerce business running profitably.