What an e-commerce CPA does
An e-commerce CPA makes sure your books show gross sales, then fees, refunds, chargebacks and reserves separately, with each payout reconciled to the bank. Without that, revenue and expenses are both understated.
They set up inventory and cost of goods sold, including freight and duties, review where you have sales tax nexus by channel and state, reconcile Forms 1099-K to your books, and prepare your income tax returns and plans, including whether an S corp fits.
For a full overview of the topic, see our e-commerce taxes and accounting guide, and for Shopify specifically, CPA for Shopify stores.
How to verify an e-commerce CPA’s license
- CPAverify. Search the CPA and the firm on NASBA’s CPAverify for license status, issuing state and reported discipline.
- State board. If the state is not on CPAverify, use the board listed in NASBA’s state board directory.
- IRS preparer directory. Confirm the credential in the IRS Directory of Federal Tax Return Preparers. Many e-commerce bookkeepers are not CPAs; that is fine for bookkeeping, but not for signing as a CPA.
Questions to ask an e-commerce CPA before hiring
- How do you reconcile marketplace payouts, including fees, refunds and reserves, to gross sales?
- How do you track inventory and cost of goods sold, and which tools do you support?
- How do you decide where I have sales tax nexus, and which states my marketplaces already collect for?
- Will you reconcile my 1099-Ks to my books?
- Do you handle bookkeeping and tax, or coordinate with my bookkeeper?
- Which channels do most of your clients sell on?
Free checklist
Sales Tax Nexus Tracker
Red flags
- Books record bank deposits as revenue, so fees and refunds disappear.
- “The marketplace collects all your sales tax” when you also sell on your own site.
- No inventory method discussed, or inventory expensed when bought.
- No awareness of economic nexus after South Dakota v. Wayfair.
- No license you can find on CPAverify or the state board.
Why clients choose Your Virtual CPA
- Licensed CPA firm working with online sellers nationwide, virtually.
- E-commerce services: e-commerce accounting, Amazon seller accounting, Shopify bookkeeping and sales tax nexus reviews.
- Transparent fees quoted upfront, in writing.
- Free initial consultation before you decide.
How it works with us
Best for: sellers with inventory, more than one channel, or customers in many states.
- Free initial consultation. Tell us your channels, apps and what is not working.
- Fees quoted upfront, in writing. Scope and fees in an engagement letter before work starts.
- Setup review. Channel reports, connected apps, chart of accounts and inventory method.
- Clean books. Payout clearing, cost of goods sold and sales tax that ties to filings.
- Ongoing. Monthly reporting, quarterly planning and year-end returns.
Connector app only vs bookkeeper vs e-commerce CPA
| Connector app only | Bookkeeper | E-commerce CPA | |
|---|---|---|---|
| Settlement and payout reconciliation | Posts summary entries | Records and reconciles | Reviews and fixes the method |
| Inventory and cost of goods sold | Uses the costs you enter | Records purchases | Sets the costing method |
| Sales tax nexus analysis | No | Rarely | Yes |
| Income tax return | No | No | Yes |
| Tax planning and entity choice | No | No | Yes |
| IRS and state notices | No | No | Yes, including representation |
Expert CPAs. Personal attention.
Payouts, inventory or sales tax not adding up? Request a free initial consultation and talk to a CPA about your store.
Frequently asked questions
Verify the license on CPAverify or your state board, then ask how the CPA reconciles marketplace payouts, tracks inventory and cost of goods sold, and decides where you have sales tax nexus. Experience with your channels, such as Amazon, Shopify or Etsy, matters more than location.
Once you hold inventory, sell on more than one channel or have real profit to plan around, usually yes. Amazon reports sales and collects sales tax as a marketplace facilitator in many states, but it does not cost your inventory, decide your income tax nexus or file your return.
Not always. Marketplace facilitator laws make marketplaces collect tax on sales made through them in states that have those laws. Sales on your own website are generally yours to handle where you have nexus. A CPA reviews each channel and state.
Form 1099-K reports gross payments, before fees, refunds and other deductions. Your books should show gross sales and each deduction separately. A CPA reconciles the two so the return explains the difference.
After the Supreme Court’s 2018 decision in South Dakota v. Wayfair, states can require remote sellers to collect sales tax based on sales into the state, even with no physical presence. Thresholds differ by state and should be checked against each state’s revenue department.
Yes. E-commerce sellers usually sell into many states anyway. Your Virtual CPA, a licensed CPA firm, works with online sellers nationwide using your marketplace reports, payouts and bank data.
It depends on order volume, number of channels and states, inventory and the state of your books. Your Virtual CPA quotes transparent fees upfront, in writing, after a free initial consultation.
Sources
- NASBA CPAverify
- IRS: Understanding your Form 1099-K
- South Dakota v. Wayfair, Inc., 585 U.S. 162 (2018)
- Streamlined Sales Tax Governing Board
- IRS: Choosing a tax professional
General information as of October 20, 2026. Tax rules change; talk to a CPA about your situation.