E-commerce accounting — multi-channel reconciliation, economic nexus, landed-cost COGS
E-Commerce

Your Revenue Is Real.
Your COGS
Should Be Too.

E-commerce accounting is not like regular business accounting. Inventory, platform fees, sales tax nexus, and multi-channel reconciliation require specialized systems — and most bookkeepers don't have them.

Platforms We Work With
Shopify
Amazon FBA/FBM
Etsy
WooCommerce
BigCommerce
eBay
TikTok Shop
Walmart Marketplace
+ direct-to-consumer, subscription boxes, and custom storefronts
Who We Work With
$100K–$10M+
Annual Revenue
Gross merchandise volume
10–10,000+
SKU Count
Single or multi-SKU catalog
1–5+ platforms
Channels
Omnichannel sellers
COGS & cash flow
Common Challenge
Inventory timing gaps
The Real Problems

What's Actually
Costing You Money

E-commerce accounting problems don't show up as obvious errors — they show up as margin compression, cash crunches, and tax surprises.

Common
Landed cost distortion
Sellers without tracked landed costs often see margin distortion that isn’t visible from bank deposits
Growing
Multi-state tax exposure
Economic nexus rules vary by state — thresholds and obligations change frequently
Frequent
Unreconciled platform fees
Payout reconciliation gaps create fee leakage that compounds over time
Problem
Why It Matters
Category
Inventory Valuation Chaos

COGS is the most important number in your business — and the hardest to track. When inventory moves across warehouses, platforms, and fulfillment centers, most sellers have no idea what their actual cost of goods sold is.

Inventory
Platform Fee Reconciliation

Amazon, Shopify, and Etsy all net out fees, refunds, chargebacks, and advertising costs before depositing. Reconciling these payouts to actual revenue is a full-time job without the right systems.

Revenue
Sales Tax Nexus Exposure

Economic nexus rules mean you may owe sales tax in states where you've never set foot. With 45 states collecting sales tax and different thresholds, this is one of the fastest-growing compliance risks for e-commerce sellers.

Tax
Cash Flow vs. Profit Confusion

You're growing fast and revenue looks great — but cash is always tight. The culprit is usually inventory purchases, platform payout timing, and advertising spend that outpaces collections.

Cash Flow
COGS Accuracy

If you're not tracking landed cost (product + shipping + duties + prep fees), your COGS is wrong. That means your gross margin is wrong, your pricing decisions are wrong, and your taxes may be wrong.

Margin
Multi-Channel Revenue Consolidation

Selling on Amazon, Shopify, and Etsy simultaneously means three different reporting systems, three different payout schedules, and three different fee structures — all needing to be consolidated into one P&L.

Revenue
Returns & Refund Accounting

High return rates (common in apparel, electronics, and home goods) create complex accounting entries that most bookkeepers handle incorrectly — overstating revenue and understating COGS.

Revenue
Advertising Spend Attribution

Amazon PPC, Meta ads, and Google Shopping spend needs to be tracked against revenue by campaign and product. Without this, you can't tell if your advertising is profitable.

Profitability

What Are You Trying to Solve?

E-commerce sellers come to us at very different stages. We work with all of them.

Get the Books Right

Your current books are a mess of bank feeds and guessed COGS. You need clean, accurate financials before you can make any real decisions. We start here.

Understand Your Margins

You're selling a lot but profit is elusive. We build the product-level margin analysis that shows you exactly which SKUs are making money and which ones are eating it.

Scale Without Breaking

You're growing fast and the financial systems that worked at $500K won't work at $5M. We build the infrastructure — inventory systems, cash flow forecasting, tax strategy — that scales with you.

The Goal State

What a Profitable E-Commerce
Operation Looks Like

Most sellers are flying blind on margin. They know their revenue. They don't know their profit. Here's what it looks like when the financial infrastructure is built correctly.

“We thought we were profitable. Turns out we were subsidizing our worst SKUs with our best ones. Once we could see it, we cut the losers and margins jumped 12 points.”

— E-Commerce Client, 3-Platform Seller

01

COGS Accurate to the SKU

Every product has a true landed cost: purchase price, freight, duties, FBA fees, returns. Margin is calculated at the SKU level, not the store level.

02

Inventory Reconciled Monthly

Your books match your warehouse. Shrinkage, returns, and write-offs are tracked. You're not discovering a $40K inventory discrepancy at year-end.

03

Sales Tax Exposure Mapped

You know which states you have nexus in, what you owe, and you're filing on time. No surprise assessments. No back-tax liability building in the background.

04

Cash Flow Forecasted 90 Days Out

You know when the next inventory buy hits, when the Amazon payout lands, and what your cash position will be. No more guessing before a reorder.

What We Do

Services for E-Commerce Sellers

We work in three stages: get the foundation right, then build visibility, then optimize for growth.

Need a one-time project? Our Advisory Services menu includes à la carte projects like COGS cleanup, sales tax nexus analysis, and inventory system setup — priced transparently.

01Setup

The foundation. Clean books, correct COGS methodology, and inventory reconciliation so your numbers actually mean something.

COGS methodology setup & cleanup
Inventory reconciliation & write-off tracking
Chart of accounts for e-commerce
Platform integration (Shopify, Amazon, WooCommerce)
02Monthly

The rhythm. Monthly close, margin reporting by SKU/channel, and sales tax monitoring so nothing builds up in the background.

Monthly bookkeeping & close
SKU-level margin reporting
Sales tax nexus monitoring & filing
Payroll & contractor payments
03Growth

The strategy layer. Cash flow forecasting, inventory financing, and tax planning for sellers ready to scale.

Cash flow forecasting & inventory planning
Multi-entity & brand structure
S-corp election & owner tax strategy
Controller services for $2M+ sellers
The Transformation

What Changes When We Work Together

BEFORENo idea what actual COGS is — margin is a guess
AFTERLanded cost tracked per SKU, real gross margin by product
BEFOREAmazon payouts don't match what was expected
AFTEREvery payout reconciled with full fee breakdown
BEFORESales tax exposure in 12 states, no compliance system
AFTERNexus analysis complete, filing calendar in place
BEFORERevenue growing but cash is always tight
AFTER13-week cash flow forecast tied to inventory purchase cycles
BEFOREMulti-channel books are a mess of duplicate entries
AFTERSingle consolidated P&L across all platforms
Sales Tax Warning

Economic Nexus Is the Biggest Hidden Risk for E-Commerce Sellers

Since the 2018 South Dakota v. WayfairSupreme Court decision, states can require you to collect and remit sales tax based on economic activity alone — even if you've never set foot there. Most states have thresholds of $100K in sales or 200 transactions.

If you're selling across state lines and haven't done a nexus analysis, you may have exposure you don't know about. We help you understand your risk, get compliant, and set up automated filing going forward.

45
States with sales tax
Each with different thresholds, rules, and filing deadlines
Get a Nexus Analysis

Integrations & Software

We work with the tools you already use — or help you choose the right ones.

Accounting
QuickBooks OnlineXeroWave
E-Commerce Sync
A2XFinaloopWebgilityTaxomateLink My Books
Sales Tax
TaxJarAvalaraQuaderno
Inventory
Cin7SkubanaLinnworksInventory PlannerBrightpearl
Payments
StripePayPalSquareShopify Payments
Payroll
GustoADPRippling
Client Results

What We've Done for E-Commerce Brands

Real outcomes from real e-commerce businesses — not projections.

InventoryCOGS corrected

Shopify Brand — $3.2M, Montana

Rebuilt inventory costing from scratch after discovering 18 months of incorrect COGS calculations. Restated financials, corrected tax returns, and implemented real-time inventory tracking.

Tax Strategy$19K saved

Amazon FBA Seller — $1.8M

Corrected multi-state nexus filings, restructured to S-corp, and implemented quarterly estimated tax planning. Net savings of $19K in year one plus eliminated $4K in penalty exposure.

Financing$2.1M credit line

DTC Brand — $5.4M, Colorado

Built lender-ready financials with clean inventory valuation and a 3-year cash flow model. Secured a $2.1M revolving credit line to fund peak season inventory purchases.

Client Testimonials

What E-Commerce Brands Say

Our COGS were wrong for 18 months and we didn't know it. 406 found it, fixed it, and restated our financials. We were overpaying taxes and underpricing products. Both problems solved.

Jessie T.
Shopify Brand Owner, $3.2M, Montana

Amazon FBA accounting is a nightmare — reimbursements, FBA fees, inventory adjustments. 406 was the first accountant who actually understood it. Clean books, correct taxes, no drama.

Ryan M.
Amazon FBA Seller, $1.8M
Common Questions

Frequently Asked Questions

Ready to Know What You're Actually Making?

Whether you're a solo Etsy seller or a multi-channel brand doing $5M, we build the financial systems that turn your sales data into real business intelligence.

Serving e-commerce sellers across Montana and the Mountain West — and nationwide for remote engagements.

Tools & Systems

Automate Your Back Office

We connect your Shopify, Amazon, or WooCommerce store to your accounting, CRM, and fulfillment workflows — eliminating manual reconciliation and giving you real-time margin visibility by SKU and channel.

Explore Business Systems