Talk to a CPA today — Free E-commerce Bookkeeping Review
Outsourced Bookkeeping for E-commerce & Retail — Shopify, Amazon & Stripe Reconciled, Sales Tax Handled
Stop staring at one $42,000 Shopify payout wondering what it actually means. ProAxis is a CPA-led bookkeeping team that reconciles every marketplace settlement, runs your multi-state sales-tax compliance, tracks real COGS and inventory, and shows you contribution margin by channel — all in a QBO file you can trust.
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The 6 Bookkeeping Problems Every Multi-Channel Seller Has
Every e-commerce we onboard arrives with one of these problems. Most arrive with several. Here’s how a CPA-led bookkeeping team fixes them.
Your Shopify or Amazon payouts hit the bank as one number and your books just show 'Sales: $42,103' — with no idea what the gross sales, fees, refunds, or sales tax actually were.
How we fix it
We reconcile every payout to its underlying transaction set: gross sales, refunds, marketplace fees, processing fees, sales tax collected, and chargebacks — all booked to the right accounts. Your P&L finally tells the truth.
You hit South-Dakota-v.-Wayfair sales-tax nexus in 6 states last year and you have no idea where you owe.
How we fix it
We run a multi-state nexus analysis against current economic-nexus thresholds, register you in the states where you've crossed, and coordinate filings with your sales-tax software (TaxJar, Avalara, Anrok, etc.).
You don't know your real gross margin because COGS is just “whatever I paid suppliers this month” instead of “cost of what we actually shipped this month.”
How we fix it
We implement proper inventory and COGS accounting: periodic or perpetual method matched to your business, COGS recognized on sale (not on purchase), inventory reconciled to your A2X / Inventory Lab / Cin7 feed.
Marketplace fees, ad spend, and 3PL costs are all in one bucket called 'Selling Expenses' and you can't see channel-by-channel profitability.
How we fix it
We track contribution margin by channel — Amazon vs. Shopify vs. Walmart vs. wholesale — with marketplace fees, ad spend (Google / Meta / Amazon), and fulfillment costs allocated correctly.
Inventory in 3 warehouses (your garage, an Amazon FBA, a 3PL) and the QBO inventory balance hasn't matched reality in 2 years.
How we fix it
We perform a reset to actual inventory at onboarding, then maintain monthly inventory reconciliation against your operations system (FBA, ShipStation, ShipBob, Cin7) so the QBO balance stays trustworthy.
Stripe / PayPal / Shop Pay all charge processing fees on different schedules and your books are missing thousands in fees you never deducted.
How we fix it
We capture every processor fee — Stripe, PayPal, Shop Pay, Amazon Pay, Square, Affirm — net of any chargeback adjustments. Most clients recover meaningful fee deductions in their first reconciliation.
What’s Included
What's Included in E-commerce Bookkeeping
Shopify / Amazon / Stripe Reconciliation
Every payout matched to underlying gross sales, fees, refunds, and sales tax. A2X-style accuracy.
Multi-State Sales-Tax Nexus Analysis
Current economic-nexus threshold tracking, registration recommendations, sales-tax software coordination.
Inventory & COGS Accounting
Proper periodic or perpetual method, COGS booked at sale, inventory tied to your operations system.
Channel-by-Channel Contribution Margin
Amazon vs. Shopify vs. wholesale vs. retail — marketplace fees and ad spend allocated by channel.
Marketplace Fee & Ad Spend Tracking
Amazon referral, FBA, storage, ad spend (Google / Meta / TikTok / Amazon) booked separately.
Multi-Currency Support
If you sell internationally, we handle FX gain/loss and revaluation correctly.
1099-K vs. Books Reconciliation
We reconcile 1099-K from each marketplace / processor to your books so 1099-K mismatch letters don't surprise you.
Monthly Financial Package
P&L by channel, balance sheet, cash flow, and a CPA-narrated review by the 15th.
Tax-Ready Year-End Close
Inventory closed, accruals booked, depreciation done — ready for the business return.
Why ProAxis
Why E-commerce Operators Switch to ProAxis
We Speak A2X, Cin7, ShipStation — Not Just QuickBooks
Most bookkeepers don't understand how Shopify settlements work, much less Amazon FBA's monthly summary. We work with the e-commerce stack (A2X, Link My Books, Cin7, Inventory Lab, ShipStation, TaxJar, Anrok) every day — so the data flowing into QBO is already structured for sellers, not retrofitted from a service-business template.
Multi-State Sales Tax: Real Help, Not Just “You Should Talk to Avalara”
We run nexus analyses, advise on voluntary disclosure programs in states where you owe past tax, register you in new states, and coordinate filings. Sales tax is the most underestimated risk for growing e-commerce sellers and we treat it as a first-class problem.
IRS Tax Resolution Specialists On Staff
1099-K mismatches, sales-tax nexus assessments from state DORs, payroll-tax notices for multi-state employees — e-commerce generates a lot of mail. As an Authorized IRS e-File Provider with a full Tax Resolution practice, we represent you when notices arrive.
100% Virtual — Built for Online-Native Operators
Your business runs in browser tabs and cloud apps. So does ours. Secure portal, QBO, monthly Zoom — no in-person meetings, no “drop off your shoebox of receipts.”
E-commerce Bookkeeping — Frequently Asked Questions
Do you use A2X / Link My Books for Shopify and Amazon?
Yes. We strongly recommend A2X (or Link My Books) for any seller doing meaningful volume on Shopify, Amazon, eBay, Etsy, or Walmart Marketplace. These tools split each marketplace settlement into its accrual-accurate components — gross sales, refunds, marketplace fees, sales tax, FBA inventory adjustments — and post the journal entry to QBO. We set them up correctly during onboarding (most clients arrive with poorly-configured A2X) and reconcile them monthly. If you're not on one of these tools yet, we'll quote the setup as part of the engagement.
How do you handle multi-state sales tax?
We run a current-state nexus analysis at onboarding using historical sales data, identify states where you've crossed the economic-nexus threshold, advise on registration vs. voluntary disclosure for past-due exposure, register you where appropriate, and coordinate filings through your sales-tax software (TaxJar, Avalara, Anrok, Numeral). For NJ-based sellers, we also handle the NJ resale certificate and any in-state physical-presence considerations. Sales tax is one of the highest-risk and most ignored areas for growing e-commerce businesses — we treat it as a first-class concern.
Can you handle inventory accounting properly?
Yes. The right inventory method depends on your business — perpetual makes sense for high-SKU or FBA-heavy sellers using Cin7, Inventory Lab, or similar; periodic with monthly true-up works for low-SKU operations. We implement either, reconcile inventory monthly to the operations system of record, and recognize COGS at the time of sale (not at the time of purchase). The result is a real gross margin number you can trust for decision-making.
We sell on multiple channels — Amazon, Shopify, wholesale. Can we see profitability by channel?
Yes. We use QBO classes (or Locations) to track each sales channel separately. Marketplace fees, ad spend, and any channel-specific costs are allocated to that channel. The result is a contribution margin by channel — so you can see whether Amazon is actually more profitable than Shopify after FBA and PPC costs, or whether wholesale margin is worth the lower revenue.
Do you reconcile 1099-K to our books?
Yes. Each marketplace and processor — Amazon, Shopify Payments, Stripe, PayPal, Shop Pay — issues a Form 1099-K. The IRS uses these to detect underreporting. We reconcile each 1099-K to your books at year-end so the gross-receipts number on your tax return matches (or has documented reconciling items). This single reconciliation prevents the most common IRS notice e-commerce sellers receive: the CP2000 1099-K mismatch.
What does monthly e-commerce bookkeeping cost?
Pricing scales with channel count, monthly transaction volume, and inventory complexity. A single-channel Shopify seller doing under $1M annual revenue typically runs $500–$900/month. A multi-channel seller (Shopify + Amazon + wholesale) doing $3M–$10M runs $1,200–$2,800/month. Catch-up bookkeeping is quoted separately. After a free discovery call we provide a fixed monthly fee.
Ready for Books That Match What Your Marketplace Reports?
Free 30-minute review of your Shopify / Amazon / Stripe reconciliation and multi-state sales-tax exposure. We'll tell you exactly what's at risk and what cleaning it up costs — no obligation.
Serving e-commerce and retail businesses across New York, New Jersey & Pennsylvania — 100% virtual.
More ProAxis Resources for E-commerce Sellers
- E-commerce Industry CPA Hub →
- E-commerce Multi-State Sales Tax Deep Dive →
- Curated Resource Hub for E-commerce Sellers →
- Case Study: 90-Day Cash Flow System →
- Bookkeeping Cost Calculator → Quick monthly-fee estimate
- Catch-Up Bookkeeping Calculator → One-time project cost if you're months behind