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Ecommerce bookkeeping services for Shopify and Amazon sellers.

Our ecommerce bookkeeping services start where your payouts end. Shopify and Amazon pay you net of fees, refunds and reserves. We rebuild the gross sale behind every deposit, cost each SKU at its landed price, and close your month by the 10th.

See the channel work

Multi-channel · March close

Net revenue $212,220

Reconciled
GrossFeesNet
  • Shopify$128,400-$4,610$123,790
  • Amazon$96,250-$27,180$69,070
  • Etsy$21,900-$2,540$19,360
  • Payouts matched to deposits142 of 142
  • COGS posted by SKU318 SKUs
  • Refunds and chargebacks split out$6,240
  • Nexus thresholds checked50 states
  • A2X
  • Shopify
  • Amazon
  • Stripe
  • QuickBooks

Certified on the platforms your business already runs on

  • Intuit QuickBooks ProAdvisor Certified Level 1
  • Intuit QuickBooks ProAdvisor Certified Level 2
  • Gusto Payroll Certified
  • Xero Payroll Certified
  • ISO 9001:2015 Certified Company
  • GDPR Compliant
  • ISO 27001:2022 Certified Company
  • AICPA SOC 2 Type II audited
  • HIPAA compliant

Where a marketplace deposit hides the real margin.

A deposit from Amazon or Shopify looks like sales. It is really sales minus fees, refunds, ad spend and reserves. Each problem below starts inside that gap, and QuickBooks will not flag any of them.

  • 01

    Four channels, four payout formats

    Shopify pays daily or weekly. Amazon settles about every two weeks. Etsy and eBay each use their own report layout.

    What it costs you

    Sales get counted twice or not at all, and the bank never ties out.

  • 02

    Economic nexus crossed without notice

    Economic nexus is the sales level that makes you owe a state's sales tax. Many states set it at $100,000 a year.

    What it costs you

    Back tax, interest and penalties arrive before you knew you had to register.

  • 03

    COGS posted at the invoice price

    Cost of goods sold (COGS) should carry the full landed cost. That is the unit price plus freight, duty and inbound fees.

    What it costs you

    Every margin reads high, so you price too low and reorder the wrong SKUs.

  • 04

    Processor deposits booked as sales

    Stripe, PayPal and Shopify Payments take out fees, refunds and chargebacks before the money lands.

    What it costs you

    Fees vanish from the P&L, and sales look smaller than they were.

  • 05

    Stock split across three places

    Units sit in your own space, at a 3PL (a third-party fulfillment warehouse) and inside Amazon FBA.

    What it costs you

    Inventory on the balance sheet drifts from what is on the shelf, and a lender spots it first.

  • 06

    Refunds landing in the wrong month

    A March order refunded in April cuts April's sales. Partial refunds and replacement units make it worse.

    What it costs you

    No two months compare, and a strong month can look weak.

  • 07

    Gift cards counted as sales

    Gift cards, store credit and preorders are cash you hold for goods not yet shipped. That is a debt, not revenue.

    What it costs you

    Sales look inflated now, and what you owe customers stays off the books.

  • 08

    Shipping and 3PL fees in one bucket

    Postage, boxes, pick and pack fees and 3PL storage rise and fall with order volume.

    What it costs you

    Cost per order stays hidden, so free shipping thresholds get set by feel.

  • 09

    Promo codes that eat the margin

    Discount codes, bundles and Amazon coupons change what you keep on each order.

    What it costs you

    A sale that lost money can read as your best week.

01 of 09

What our ecommerce bookkeeping services cover for each sales channel.

A single monthly fee covers every step, from raw settlement reports to a CPA-ready file. Order volume never changes the price, and nothing listed is extra.

Sales, payouts and refunds

Each marketplace and processor tied out on its own before any channel joins the total.

Settlement report reconciliation
Amazon, Shopify, Etsy, eBay and Walmart reports split into gross sales, fees and holds.
A2X or Link My Books mapping
Each payout mapped to the right accounts and dates, not posted as one lump deposit.
Processor clearing accounts
Stripe, PayPal and Shopify Payments run through a holding account so fees show alone.
Refunds and chargebacks by order
Each one tied to its original order and dated to the month it belongs in.
Online seller checking an order on her phone beside packed shipping boxes

Inventory, COGS and 3PLs

The numbers that show which products earn their shelf space and which only move cash around.

Landed cost per SKU
Unit price, freight, duty, broker fees and FBA inbound fees built into each unit.
Stock counts across locations
Warehouse, 3PL and FBA units tied to the books each month, with shrinkage written off.
Fulfillment cost per order
Postage, packaging, pick and pack and storage tracked so each order has a real cost.
Margin by channel and SKU
Gross margin after marketplace fees, shown for each channel and each product line.
Warehouse racking stacked with cartons of inventory

Nexus, close and reporting

The month closed on a checklist, and state tax thresholds watched before they turn into notices.

Economic nexus monitoring
Direct sales in each state checked against its threshold, apart from marketplace sales.
Deferred revenue schedules
Gift cards, store credit and preorders held as a liability until the order ships.
Statements with a margin note
P&L, balance sheet and cash flow sent by the 10th, with a short note on margin shifts.
Year-end file for your CPA
Closed books, a 1099-K tie-out and inventory schedules, ready for the return.
Store owner smiling at her laptop in front of a clothing rail

The seller apps you already run, left exactly as they are.

We log in to the channels, processors and sales tax tools you use today. You keep your apps and your QuickBooks or Xero file, and your store runs the same way.

ShopifyAmazonEtsyeBayWalmartWooCommerceBigCommerceStripePayPalSquareA2XQuickBooksXeroOracle NetSuiteAvalaraTaxJar

Get your true marginon your top ten SKUs

Tell us how you sell. We will read one month of real payouts and your COGS setup, show where the numbers go wrong, and send a flat monthly price. It costs nothing, and you owe us nothing after.

  1. A written list of where payouts and COGS are posted wrong.
  2. Your direct sales checked against each state's nexus threshold.
  3. Landed-cost margin on your ten best-selling SKUs.
  4. Your flat monthly price and scope, in writing, within 24 hours on business days.

Covered from day one

  • Payouts
  • Landed cost
  • Nexus
  • Margin

Your sales channels and a rough order count are all we need to start.

Amazon and Shopify errors that skew pricing and tax.

Each one bends a different choice: what you charge, where you sell and what you owe. All three start when an online store is booked like a shop with one cash register.

Amazon and Shopify errors that skew pricing and tax.
01Posting the net payout as salesWhat it causesFees, refunds and reserves vanish into one number. Sales look smaller, costs look lower, and no P&L line traces back to an order.How we handle itWe work from the settlement report, not the deposit. Gross sales, each fee, refunds and holds post on their own lines, and the total ties to the bank.
02Assuming Amazon covers all your sales taxWhat it causesMarketplace facilitator laws make Amazon, Etsy and Walmart collect and remit tax on their own sales. Orders on your Shopify site are still yours to track.How we handle itWe count your direct sales by state, apart from marketplace sales. You get a written warning as any threshold gets close.
03Costing stock at the supplier priceWhat it causesFreight, duty and FBA inbound fees sit in overhead, so every SKU looks better than it is. The de minimis rule, which let parcels under $800 skip duty, ended in August 2025.How we handle itWe build landed cost per SKU from each shipment and match it to each sale. Margin per product becomes a number you can set prices on.

Figures that trace back to a single order.

Plenty of ecommerce accounting services stop at a P&L. We add a second review on every close and a price that stays flat as orders grow.

Payouts tied to the bank
Per channel
Landed cost built
Per SKU
Direct sales tracked
Every state
Store P&L in your inbox
10th

Ecommerce accounting metrics sent with every close.

Three statements tell you what happened. These six figures tell a seller what to do next, and each one comes with a plain note on why it moved.

Every month

Arrives with the P&L, so ad budgets, prices and reorders are set on this month's numbers.

  • Measures: Sales less landed cost and marketplace fees, per channel

    Why it matters: The same SKU often earns more on Shopify than on Amazon. This shows where the next unit should sell.

  • Measures: Order revenue less landed cost, shipping, fees and payment costs

    Why it matters: Sets a free shipping threshold and a bundle price that still leave a profit.

  • Measures: Refunds and returns as a share of gross sales, per product

    Why it matters: A rising rate on one SKU points to a listing or quality issue. Catching it early beats a one-star review.

Every year

Pulled at year end. These are the first figures a buyer of your brand will ask to see.

  • Measures: COGS divided by average inventory on hand

    Why it matters: Shows how much cash sits in stock that does not sell. That is often the largest sum you can free up.

  • Measures: Change in sales by marketplace and by your own site

    Why it matters: Splits real growth from one algorithm change. Buyers and lenders test this first.

  • Measures: Total ad cost of sales: all ad spend divided by all sales

    Why it matters: Shows whether ads grow the brand or just buy sales you would have made anyway.

Store books built from deposits and books built from settlements.

Deposit-based books are common, and not every line in them is wrong. They fail in the same five places once you sell on more than one channel.

Books posted from payoutsWith Twelix
  • Amazon payoutsOne deposit posted as salesGross sales, fees and holds split out
  • Product costSupplier bills expensed when paidLanded cost matched to each sale
  • Sales taxLeft to the marketplaceDirect sales checked by state
  • StockCounted once a year, if at allTied out monthly at 3PL and FBA
  • ReportsA P&L and a balance sheetMargin per channel, SKU and order

From your first settlement report to a close every month.

Setup comes first: payouts remapped, landed cost built and clearing accounts fixed. Then the close runs on the same dates every month.

Takeover

Reading your channels

Once, before the first close
  1. 01

    Day 0

    A look at one real payout

    A 30-minute call on how you sell. We open a recent Amazon or Shopify payout and check how it was posted. We also check whether COGS is landed or invoice priced, and which states you may owe.

  2. 02

    Day 1

    One price for every channel

    A single monthly fee covers all your channels. If past months need fixing, that cleanup is priced on its own. Both arrive in writing.

  3. 03

    Day 2

    A2X and chart of accounts audit

    You grant access to your books and channels. Before we touch a transaction, we check the A2X mapping, clearing accounts and inventory items.

  4. 04

    Week 2

    Opening balances you can trust

    Settlements are remapped, landed cost is built per SKU and gift cards move to a liability. Every channel then ties to the bank.

Monthly

The payout-to-P&L close

Same dates, every payout month
  1. 01

    Daily

    Payouts coded as they settle

    Channel payouts, processor deposits, supplier bills and stock moves are coded as they arrive. Nothing waits for month end.

  2. 02

    Day 5

    Each channel tied to the bank

    Every marketplace and processor is matched on its own terms. Refunds go to the right month, and stock ties to the count.

  3. 03

    Day 8

    Second review and margin check

    Someone other than the preparer checks the close. Margin is rerun by channel and SKU, and direct sales are checked against state thresholds.

  4. 04

    Day 10

    P&L, margin pack and a short note

    You get the P&L, balance sheet and cash flow with margin reports. A short note says what moved and what needs your call.

Each new month starts from the last reconciled payout.

Seller costs we record in the month they happen.

Each cost below is coded and backed up through the year. Your tax preparer gets a finished file, not a pile of Amazon reports in March.

  • Shipping and 3PL fees

    Postage, packaging, 3PL storage and pick fees, and carrier fuel surcharges.

  • Marketplace and app fees

    Shopify plans, Amazon referral and FBA fees, apps, email tools and inventory software.

  • Ads and promotion

    Meta, Google Shopping and Amazon Sponsored Products spend, plus affiliate and creator payouts.

  • Listing photos and video

    Product shoots, studio time, samples made for listings and editing software.

  • Unsellable returns

    Damaged, expired or unsellable units written off, with the Amazon removal or disposal report as proof.

  • Home office and storage

    The business share of rent, power and internet, plus a storage unit used only for stock.

01 of 06

Whether and how each one is claimed depends on your entity and your facts. We book them, and your CPA decides how they are claimed.

Real stories from business owners.

Owners who moved their books to Twelix, on what changed afterward.

Eric Wexler, Obsedian Media LLC
Chad Fischman, Fischman Asphalt
Amy Stone, Guru Pet Company
Prathan Powell, The Black In HR
Eric Wexler, Obsedian Media LLC
Chad Fischman, Fischman Asphalt

01 of 04

What sellers ask about ecommerce bookkeeping services.

  1. Yes, we reconcile each platform on its own settlement report first, then combine them into one P&L. Shopify, Amazon, Etsy, eBay, Walmart and TikTok Shop each pay on different dates and in different formats. Keeping them apart until the end is what lets you see margin by channel. Merged channel sales are a common reason a seller cannot tell which marketplace makes money.

  2. Yes, we track your sales tax exposure each month. We can prepare the returns and hand them to your CPA, or file them for you if you ask and give us access. Since the 2018 South Dakota v. Wayfair ruling, states can tax remote sellers once sales pass an economic nexus threshold. Many states set it at $100,000 a year, and a few set it higher. Marketplace facilitator laws make Amazon, Etsy and Walmart collect tax on their own sales. Your Shopify site sales are not covered, so we count them by state. States change these rules often, so we flag the risk and your advisor makes the call.

  3. We post each return or chargeback against its original order and date it to the right month. Restocking fees, partial refunds, replacement units and chargeback fees each get their own line. Returned units that can be resold go back into stock. Units that cannot are written off, with Amazon's removal or disposal report as proof. This keeps a heavy-return month comparable to a quiet one.

  4. Yes, we work with A2X, Link My Books, Shopify reports and Amazon Seller Central settlement reports. We check any existing mapping before we trust it, because one bad rule misposts every payout it touches. We also work with Stripe, PayPal, Square, Avalara and TaxJar. The ledger stays in QuickBooks Online, Xero or NetSuite, whichever you already use.

  5. Yes, we track COGS per SKU or per product family, built from landed cost. Landed cost is the unit price plus freight, duty, customs broker fees and inbound fees. We match that cost to each sale, not to the day you paid the supplier. Duty rates changed often in 2025, so we update landed cost with each new shipment. The result is a margin per product you can set prices on. For Guru Pet Company, fixing product mappings and inventory moved reported gross profit from 31% to 54%.

  6. Bookkeeping for ecommerce records an online store's sales, fees, inventory and taxes so the books match each payout and the bank. It differs from regular bookkeeping in three ways. Sales arrive net of fees, stock sits in several places, and sales tax depends on where buyers live. Good ecommerce books split every payout back into gross sales, fees and refunds.

  1. Amazon seller bookkeeping splits each settlement report into sales, referral fees, FBA fees, storage fees, refunds and reserves, and books each one separately. Settlements usually run on a 14-day cycle that rarely matches your month end, so we split each one across the right months. Amazon also holds some funds until about seven days after delivery, and we track that hold as money owed to you. FBA stock still belongs to you, so we count it with the rest of your inventory.

  2. No, Shopify reports sales and payouts, but it does not keep a full set of books. It has no balance sheet, no landed cost and no bank reconciliation. It also cannot see your Amazon sales, supplier bills or loan payments. Shopify data flows into QuickBooks or Xero through A2X or a direct sync, and we reconcile it there.

  3. Accrual suits most stores that hold inventory, because it matches product cost to the month the product sells. Under the cash method, one big stock order can wipe out a good month on paper. Under accrual, that stock waits on the balance sheet until it sells. The IRS lets businesses under a gross receipts test choose, and that limit rises each year. Your CPA picks the tax method. We can keep accrual books and still give them a cash view.

  4. Twelix charges one flat monthly fee, set by your channel count, order volume, inventory setup and number of entities. The fee does not rise in a busy month or at peak season. There is no setup fee, and you can stop month to month. The price comes in writing within 24 hours of the review call. Any cleanup of past months is priced on its own.

  5. Yes, we clean up past months as a separate project with its own fixed price, before the monthly close begins. We remap old settlements, rebuild landed cost and move gift card balances to a liability. Then we tie every channel to the bank. Starting monthly work on a wrong opening balance would just carry old errors forward.

  6. You get a Form 1099-K when a platform pays you over $20,000 across more than 200 transactions in a year. The One Big Beautiful Bill Act restored that limit in 2025. The form shows gross payments before fees and refunds, so it rarely matches your net payouts. We tie each 1099-K to the books so your CPA can explain the gap. You owe tax on all income, with or without a form.

See which SKUs actually earn.

Book a free 30-minute call. Bring one recent payout and your product costs. We will show where the books go wrong and send a flat monthly price, before you sign anything.

Talk to us first

Priced flat, not per orderCancel any month