Deposits booked as sales
Net payouts recorded as revenue, with fees, refunds and ads missing from the books.
Specialty · E-commerce bookkeeping
E-commerce Bookkeeping for Amazon, Shopify & Online Sellers
Marketplace deposits hide fees, refunds, reserves and ad spend. We rebuild every payout so your revenue, margins and tax return are correct, and you finally know which channel makes money.
Why it matters
Your bank deposit is not your revenue
Amazon, Etsy and Shopify Payments pay you a net amount after taking their fees, refunds and advertising. If your books only record the deposit, revenue is understated, expenses are missing and your margins look wrong.
Marketplaces also report your gross sales to the IRS on Form 1099-K. When the books only show net deposits, the numbers do not match, and that mismatch is a common reason for IRS questions.
We break every settlement into its parts so each number in your books has a source.
One Amazon payout, unpacked
Gross product sales$18,420.00
Referral fees−$2,763.00
FBA fulfillment fees−$3,104.50
Refunds & returns−$612.40
Sponsored ads−$1,240.00
Deposited to bank$10,700.10
Example figures. Booking only the $10,700 deposit understates revenue by 42% and hides $7,720 of deductible expenses.
Problems we fix
The usual e-commerce bookkeeping mistakes
No cost of goods sold
Inventory purchases expensed when bought instead of when sold, so monthly profit swings wildly.
Unclear sales tax position
Marketplace sales mixed with sales from your own store, so you can't tell what was collected for you and what you may owe.
Numbers that don't match
Gross sales reported on Form 1099-K that don't tie to the books or the tax return.
No profit by channel
Everything lumped together, so you can't see whether Amazon or Shopify actually earns the money.
Foreign owners & currencies
Payouts in several currencies and owner transfers that also need to be reported on Form 5472. Form 5472 →
What's included
Books built for online sellers
We work with the platforms and tools you already use. If you use a connector such as A2X or Link My Books, we work with its summaries; if you don't, we reconcile the settlement reports directly.
AmazonShopifyEtsyWalmartTikTok ShopeBayStripePayPalA2XLink My Books
- Settlement reconciliation: every payout traced to gross sales, fees, refunds and reserves.
- Fees by type: referral, fulfillment, storage, advertising and payment processing.
- Inventory and COGS: landed cost, FBA fees and write-offs recorded correctly.
- Sales tax tracking: marketplace-collected sales separated from sales on your own store.
- Profit by channel, so you know which store earns the money.
- Monthly profit and loss and balance sheet.
- 1099-K tie-out at year end.
- Tax-ready books for your return, prepared by us or your own preparer.
Sales tax basics
Marketplace sales vs your own store
In most states, marketplaces such as Amazon, Etsy and Walmart are required to collect and remit sales tax on the sales they facilitate. Sales through your own Shopify store are different: once your sales into a state pass that state's economic nexus threshold, you may need to register and collect tax yourself.
We keep the two separate in your books and track your sales by state, so you can see where you may be approaching a threshold.
Behind on your books?
Catch up before tax season
Many sellers come to us with months of unreconciled payouts. We rebuild the history from the settlement reports, fix inventory and cost of goods sold, and get the books ready for the tax return.
Pricing
Starting at $199/month, quoted on your scope
The monthly fee depends on your order volume, number of sales channels and whether we track inventory. Catch-up work is quoted separately based on how many months need work.
Order volumeSales channelsInventory trackingCurrenciesMonths behind
E-commerce bookkeeping$199/mo+
Final price depends on complexity and scope.
Get a Custom Quote →
Client reviews
From product business owners
Bookkeeping
You guys are amazing!
Thorough, efficient, knowledgeable and easy to communicate with. I would recommend Shape Accounting to anyone looking for professional bookkeeping services.
Bookkeeping
Highly recommended!
Second time using the bookkeeping services of Shape Accounting. Very thorough work and highly knowledgeable staff.
FAQ
E-commerce bookkeeping questions
Selling on more than one platform? Tell us which ones and your monthly order volume.
Why don't my Amazon deposits match my sales?
Amazon pays you a net amount after deducting referral fees, fulfillment fees, refunds, advertising and sometimes a reserve. Your real revenue is the gross sales figure, and each deduction is a separate expense. We break every settlement into those parts.
Do you work with A2X or Link My Books?
Yes. If you already use a connector such as A2X or Link My Books, we work with its summaries. If you don't, we reconcile the marketplace settlement reports directly.
My Form 1099-K doesn't match my books. Why?
Form 1099-K reports gross payment amounts, before fees and refunds. If your books only record net deposits, they will not match. We reconcile the 1099-K to your gross sales so the tax return is consistent.
Do I need to collect sales tax on my Shopify store?
It depends on where your customers are. Marketplaces usually collect sales tax on their own sales, but your own store may need to register and collect tax in a state once your sales there pass that state's economic nexus threshold. We track your sales by state so you can see where you stand.
I live outside the U.S. and sell through a U.S. LLC. Can you help?
Yes. We keep the LLC's books and also prepare the Form 5472 and pro forma Form 1120 that foreign-owned single-member LLCs must file each year.
Related services
For online sellers
Form 5472 filing
For sellers who own their U.S. LLC from abroad.
Learn more →U.S. tax preparation
Business and personal returns built on reconciled books.
Learn more →LLC formation
Start your U.S. selling business the right way.
Learn more →Free consultation
Get your books and taxes in shape
Tell us about your business. We'll reply within one business day with next steps and a custom quote.
Email info@shapeaccounting.com
Hours Monday to Friday, 9am–5pm