The Texas Comptroller has access to more data than most business owners realize. When you file your sales tax return, the numbers should match your point of sale totals, bank deposits, and accounting records. If they don’t align, you’re at risk of receiving a notice requesting explanation or being flagged for audit.

Mismatches can trigger a notice from the Comptroller asking you to explain the discrepancy. Sometimes it’s a simple error that gets resolved with documentation. Other times, the state determines you underreported and issues an assessment for additional tax owed plus interest and penalties. Texas charges penalty fees on unpaid tax and interest compounds monthly, so small gaps can become expensive quickly.

The more serious outcome is an audit. The Comptroller can review four years of records. They’ll request POS reports, bank statements, invoices, and accounting records. If your documentation is disorganized or doesn’t support the numbers on your returns, the auditor will estimate what you owe based on available information. That estimate typically favors the state, not you.

Discrepancies happen for several reasons. Refunds processed in the POS might not get reflected properly on your return. Sales from multiple channels like online orders or third-party marketplaces might not sync with your main system. Cash transactions sometimes get recorded differently than card payments. For restaurants and bars, tips can create confusion about taxable sales versus gratuities.

The Comptroller compares your reported sales tax to data from other sources. For businesses selling through Amazon, Etsy, or other marketplaces, those platforms report sales directly to the state. Bank deposits provide another reference point. If you report $50,000 in taxable sales but bank deposits and marketplace reports show $65,000 in receipts, that gap needs an explanation you can document.

Prevention comes down to monthly reconciliation. Your POS sales totals should tie to bank deposits after accounting for tips, refunds, and credit card fees. Those numbers should match your bookkeeping records. When you file sales tax, you’re working from reconciled data rather than pulling a number from one system and hoping it’s accurate.

If your records already have discrepancies, catching them before a notice arrives puts you in a better position. Business tax preparation that includes reviewing sales tax filings against POS data and bank deposits helps identify problems before the state does. Filing amended returns proactively typically results in lower penalties than waiting for the Comptroller to find the issue.