5 Questions to Ask Before Hiring a CPA for Your eCommerce Business

Kimberly Green | 2026-04-14

5 Questions to Ask Before Hiring a CPA for Your eCommerce Business Most CPAs have never seen an Amazon settlement report. This is the problem. Your accountant might be great. But if they've built their practice on W-2s and dentist returns, they're probably blind to the specific financial traps that sink eCommerce sellers. For a $1M seller with basic accounting gaps, a misaligned CPA could cost you $12K-$25K a year in missed deductions and inventory adjustments. Worse: audit risk, inventory miscalculations, and multi-channel reconciliation nightmares that blow up your year-end numbers. Before you hire, ask these five questions. The answers tell you whether you're talking to someone who actually understands eCommerce accounting or someone who's going to cost you. 1. Have You Reconciled Amazon Settlement Reports Before? If they hesitate, walk. Amazon settlement reports look nothing like a business checking account. There's a time lag between when inventory sells and when Amazon deposits money. There are fees embedded in the deposit. There are chargebacks, refunds, and FBA inventory adjustments that don't match your revenue line. A generalist CPA sees the bank deposit and thinks "that's my revenue." A CPA who knows eCommerce knows that the Amazon settlement report is the source of truth, and the bank deposit is just the cash movement. If they've never reconciled one, they don't understand your business. Ask them to walk you through how they'd handle a month where Amazon deposits $50K but the settlement report shows $62K in actual sales. This is normal. If they can't explain it, that's a red flag. 2. Do You Understand Shopify Payouts vs. Earned Revenue? Here's what trips up generalist accountants: Shopify holds payments. You make a sale on Monday, but Shopify doesn't deposit the money until Friday. Meanwhile, your cash accounting is tracking deposits, not sales. If your CPA is building your accounting system around the Shopify payout deposits instead of the actual sales date, your inventory calculations and profit reports will be wrong. You'll show losses in months you made money, and profits in months you didn't, because the cash doesn't match when the goods actually left your hands. They should understand the difference between accrual accounting (recording sales when they happen) and cash accounting (recording when you get paid), and know which method actually serves your business. Most eCommerce businesses need accrual methods for inventory and sales tax purposes. A CPA who gets this wrong can leave you exposed to sales tax audits and overstate your...