Sales tax software for Shopify

Shopify can calculate and collect at checkout. It does not register you, file, or remit. That gap is worse than it sounds. Collecting tax without a permit is a bigger red flag to a state than never collecting, because the money is held in trust and the state can see it was charged. We have picked up a Shopify seller who had collected roughly $18,000 over four years and remitted none of it. Marketplaces work differently: on Amazon, Walmart, eBay, and TikTok Shop, facilitator rules put collection and remittance on the platform. Your own store is not a marketplace.

Scope. Shopify Tax calculates at checkout, free to $100,000 in sales and then 0.35% per order, 0.25% on Plus, capped at $0.99 an order and $5,000 per region a year. Its filing add-on is $75 a return, $50 on Plus, covers current periods only, and is US-only. It does not register you, chase exemption certificates, or see revenue that never touched Shopify. Commenda covers the whole lifecycle in 70+ countries. Many customers run both during the switch, then retire Shopify Tax once we are filing.

A voluntary disclosure agreement usually waives penalties and leaves interest, and the waiver succeeds in roughly 98% of the ones we run. For scale: on one $104,000 liability that had been exposed about 22 months, penalties would have run $21,000 to $31,000, against roughly $6,000 to $8,000 of interest with a VDA in place. Lookback periods are two to four years in most states and unlimited in a few, Nevada among them. Below a meaningful liability a plain backdated registration costs less than a VDA, and we will tell you which one your numbers point to.

The VDA first, wherever exposure already exists. Registering announces you to the state and lets it back-charge tax, interest, and penalties from your original nexus date. The order that protects you is: pull the Shopify order history, quantify the exposure per state, file the VDA, then register and start collecting.

Physical presence, and it catches sellers out more often than thresholds do. Inventory at a 3PL, a warehouse, a remote employee, a traveling sales rep, or an office all create physical nexus in that state, at any revenue. It also lingers: trailing nexus keeps an obligation alive after the employee or the inventory leaves. Economic nexus is the other half, usually $100,000 in sales or 200 transactions a year, and 45 states plus DC levy sales tax at all. Commenda prompts you each quarter for employee locations so a new hire does not open a state quietly.

Yes. Multi-storefront setups are natively supported, including a separate legal entity per store, and Shopify Plus is covered. You switch entities on one dashboard with consolidated registrations, exposure, and filings. Older tax integrations often could not do this without manually splitting the stores.

Every source is read separately and rolled into one exposure number, with the source visible on each transaction. Tax a marketplace already collected is tracked apart from revenue that still needs it, and we can usually see how much the platform remitted, so a direct ERP sale gets tax applied while an already-taxed Amazon order does not. Line items carry SKU, shipping amount, tax on shipping, and tax collected, so a filing traces back to the order.

Yes, and this is where B2B sellers get caught: a US business-to-business sale is taxable unless a valid certificate is on file. You need one per state you deliver into, though multi-jurisdictional certificates cover larger customers across several. Your customers upload through a self-service portal, we validate and store each one against the customer, and it applies automatically to future orders. Expiries are tracked and chased, including annual refreshes in states like Florida, and we can batch-request certificates from customers who have never sent one.

You can start collecting on the "applied for" registration number in Shopify rather than accruing more exposure while paperwork clears. Once the registration or the VDA is approved, that collection is retroactively authorised.