E-commerce Sales Tax Reporting Checklist

Export rolling 12-month gross sales and transaction counts per state from Shopify, Amazon, eBay, Walmart, and any other channel. Include marketplace-facilitator sales separately from direct-channel sales — most states count marketplace sales toward economic-nexus thresholds even when the marketplace remits.

Most states use a $100K or 200-transaction threshold post-Wayfair, but several have moved off the 200-transaction prong (CA, NY, TX use revenue only). Use Avalara, TaxJar, or Anrok's nexus dashboard rather than hand-checking — thresholds and effective dates change yearly.

Register through the state's Department of Revenue portal or via Avalara / TaxJar registration service. Do not begin collecting tax in a state before the registration effective date — premature collection without a permit is itself a violation. Update Shopify Tax / Amazon tax settings once permits issue.

Export Amazon's Sales Tax Report (Marketplace Facilitator), eBay's tax invoice, Walmart's 1099-K and tax report, and Etsy's tax report. These document tax the marketplace already collected and remitted on your behalf — most states still require you to report these as gross / exempt on your return.

Export Shopify Tax / TaxJar / Anrok report covering tax you collected directly. Reconcile against Stripe / Shopify Payments payouts to confirm collected tax matches what's actually sitting in your bank — discrepancies usually mean rounding errors, refunds not reflected, or rate-update timing issues.

Match the sales tax liability account in QuickBooks / Xero / NetSuite against collected-tax reports per state. Investigate variances over $50; common causes are mid-period rate changes, refunded orders not reversing tax, or shipping taxability mis-configured for a specific state.

Confirm tax codes for clothing, food, supplements, digital goods, and SaaS — these vary wildly by state (clothing exempt in PA / NJ / MN; supplements taxable in some states, food-exempt in others). New SKUs added since last filing especially need a tax-code review.

Generate AutoFile / draft returns in TaxJar, Avalara, or Anrok for each state. For each state, the return must show gross sales, marketplace-facilitator sales (deducted as exempt in most states), taxable sales, and tax due. Some states require county / district / local breakdowns (CA, TX, LA, CO).

Colorado, Louisiana, and Alabama have home-rule jurisdictions that file separately from the state return. Confirm each home-rule city you have nexus in is included; missing a home-rule filing is a frequent gotcha for sellers using state-only automation.

About 25 states offer a small vendor / collection allowance for filing on time (typically 0.5%–2% of tax due, capped). Easy to leave on the table if you're hand-filing or if your automation tool isn't configured for it.

Most state filing deadlines fall on the 20th of the month following the period (some on the last day, e.g. NY quarterly). File two business days early to absorb ACH issues. Keep confirmation numbers — these are your proof of timely filing if a notice arrives later.

Common rejections: bank account not pre-authorized for state ACH debit, EIN mismatch, period closed in error. Resolve before the statutory deadline — most states impose 5%–10% of tax due as a late-filing penalty plus interest accruing daily.

Notices typically have a 30-day response window; ignoring them escalates to liens or revoked permits. Most are reconcilable — period-mismatch, marketplace-facilitator sales miscoded, or rate-change timing. Log each notice with state, period, amount, and response deadline.

Pull the period's exemption certificates, resale certificates, marketplace-facilitator reports, channel-by-channel sales detail, and prior return copies. Loop in a sales-tax CPA before responding to a formal audit letter — informal responses can waive procedural rights.

Retain returns, payment confirmations, channel reports, and exemption certificates for at least 4 years (most states; CA requires 4, NY 3, some longer for unfiled-period statute). Store in a tax-period folder structure (e.g., 2025/Q3/StateXX) in a backed-up shared drive — not in an analyst's personal email.