New York e-commerce accounting that survives a sales-tax audit.

Three things a generalist bookkeeper usually misses. First, multi-state sales-tax nexus — selling across state lines creates tax obligations in states you’ve never set foot in. Second, inventory and cost of goods sold — your margin is fiction until COGS is tracked correctly per unit and channel. Third, marketplace reconciliation — the deposit Amazon or Shopify sends is net of fees, refunds, and reserves, so booking it as revenue makes your financials wrong. E-commerce accounting handles all three and reports profit by channel, not just a blended total.

When you cross a state’s economic-nexus threshold — a standard created by the 2018 South Dakota v. Wayfair Supreme Court decision, which let states require sales-tax collection based on sales volume alone, with no physical presence. Each state sets its own threshold; many use $100,000 in sales, some with a 200-transaction alternative. New York’s test, for a business located outside the state, uses “and” rather than “or”: it must register once, in the immediately preceding four sales tax quarters, its gross receipts from tangible goods delivered into New York exceeded $500,000 and it made more than 100 such sales (TB-ST-175). Storing inventory in a state, such as in an Amazon FBA warehouse, also creates nexus on its own. We track the data; your CPA confirms your nexus position and files.

For sales through a marketplace, largely yes — under marketplace-facilitator laws, platforms like Amazon, Etsy, eBay, and Walmart collect and remit sales tax on the sales they facilitate, so you don’t collect on those transactions yourself. But two traps remain. First, those marketplace sales still count toward your own nexus threshold — $400,000 through Amazon plus $150,000 through your own Shopify store into New York still crosses the $500,000 mark. Second, direct-to-consumer sales through your own website or store are your responsibility once you’ve crossed the threshold. And in New York, a marketplace seller that meets any of the sales tax registration requirements must register and file periodic returns even if a marketplace provider will remit the tax on the sales it facilitates (TB-ST-175), so the returns still need your marketplace totals. We track both, split by channel and sales tax quarter, so nothing falls through the gap.

We track landed cost per unit — what each item actually costs to acquire and bring to your warehouse, including freight and duties — and record cost of goods sold accurately as you sell, so gross margin reflects reality. Done right, you can see profitability by product and by channel, which is what tells you which SKUs to scale and which are quietly losing money after fees. For sellers on Amazon FBA or with multiple warehouses, we also keep the inventory picture consistent across locations.

Yes — it’s the heart of e-commerce bookkeeping. Each channel pays out a net figure that bundles gross sales, selling fees, refunds, chargebacks, advertising, and reserves. We break each payout into its components — often using a connector like A2X for Amazon and Shopify — and map them into QuickBooks so your books show true gross revenue, real fees, and accurate margin rather than a single net deposit. That’s also what makes your sales-tax base correct.

In New York, prewritten (off-the-shelf) software and downloaded software or video games are generally taxable, and those sales count toward your economic-nexus threshold. Most other electronically delivered content — e-books, music, streamed video — is generally not taxable in New York. Because the lines are specific and vary by what exactly you sell, we set QuickBooks to tax what’s taxable and flag the rest, and your CPA confirms taxability for your particular catalog before filing.

Monthly bookkeeping for a New York e-commerce business runs $500–$2,500+ per month, fixed-fee against a written scope. Pricing is set by order volume, the number of sales channels you reconcile, and inventory complexity — a single-channel store with light inventory is at the lower end; a multi-channel seller with FBA, large catalogs, and multi-state tracking is higher. We quote a firm number after reviewing your file.

Start with a free discovery call. We review your QuickBooks file and sales channels remotely, map your inventory model and the states you ship into, determine whether you need a cleanup first or can go straight to monthly service, and send a written fixed-fee proposal within 3 business days. Your senior bookkeeper begins as soon as you approve.