The biggest distinction Texas e-commerce sellers need to understand is how marketplace facilitator laws work. When you sell through Amazon, the marketplace collects and remits Texas sales tax for you. Amazon handles the compliance on those transactions. But when you sell directly through your own Shopify store, you’re responsible for collecting Texas sales tax from customers and filing returns with the Texas Comptroller.

This creates two different sales tax situations within the same business. Your Amazon sales are handled by Amazon. Your direct Shopify sales require you to register for a Texas sales tax permit, collect the correct rate based on where your customer is located, and file periodic returns. Many sellers don’t realize they need to handle these separately.

The reconciliation challenge is where most e-commerce bookkeeping problems start. Amazon sends payouts that combine your sales revenue, minus fees, minus refunds, plus or minus various adjustments. The sales tax Amazon collected doesn’t come to you at all. It goes directly to the state. But when you’re reconciling your books, you need to separate what was actually revenue from what were fees and what was tax.

If you record your Amazon payout deposit as revenue without breaking it out, your books will be wrong. You’ll understate revenue because the payout is net of fees, and you won’t have a clear picture of what your actual selling expenses are. This matters for understanding your margins and for tax preparation.

Refunds add another layer. When a customer gets a refund on Amazon, the sales tax is also refunded. Amazon handles this, but you need to make sure your revenue records reflect the net sales correctly. On Shopify, when you refund a customer, you need to track that the sales tax was also refunded so your sales tax return is accurate.

For Texas specifically, you should also know that some items are taxable and some aren’t. Clothing is generally taxable in Texas. Food products sold through e-commerce can get complicated depending on what’s being sold. If you’re selling across multiple categories, the tax treatment might vary by product.

Multi-state sales add complexity if you’re shipping to customers outside Texas. Each state has its own sales tax rules and thresholds for when you need to register and collect tax. Many e-commerce sellers have nexus in multiple states and don’t realize it until they get a notice.

Keeping your records clean requires separating marketplace sales from direct sales, tracking fees as expenses rather than just recording net payouts, and reconciling both to what actually hit your bank account. If you’ve fallen behind on any of this, bookkeeping cleanup and catch-up services can help get your records straight before tax time so you have accurate reporting and understand what your business is actually making.