Receiving a sales tax audit notice from the Missouri Department of Revenue (DOR) can be an unsettling experience for any business owner. The prospect of having your financial records scrutinized and facing potential back taxes, penalties, and interest is enough to cause significant stress.
However, understanding the audit process and knowing the right steps to take can make all the difference in protecting your business’s financial health.
This guide will walk you through what to do when you receive a Missouri sales tax audit notice and how to navigate the process effectively.
Step 1: Read the Audit Notice Carefully
The first and most critical step upon receiving a sales tax audit notice is to carefully review the entire document. Do not set it aside or assume it will resolve itself. The notice from the Missouri Department of Revenue will contain essential information, including:
- The specific tax periods being audited
- The type of audit (correspondence, desk, or field audit)
- The deadline for responding
- The documents you will need to provide
According to the Missouri DOR, an auditor will typically contact businesses either by phone or by letter to establish initial communication. Pay close attention to all deadlines; missing them can result in default assessments and additional penalties.

Step 2: Gather Your Records and Documentation
Once you understand the scope of the audit, begin assembling all relevant records. The burden of proof in a Missouri sales tax audit falls on the taxpayer. You will need to substantiate every number reported on your returns.
The Missouri DOR typically examines records, including the following:
- Copies of Missouri sales and use tax returns and supporting worksheets
- Sales journals, general ledgers, and source documents
- Invoices and receipts
- Exemption certificates
Missouri law requires that records be kept for at least three years, though the DOR recommends retaining records for five years. If your records are maintained electronically, providing them through the DOR’s Computer-Assisted Audit Program (CAAP) on compact disk or similar media can substantially reduce audit time at your business location.
Example: The SEBA Donut Shop Audit
The case of SEBA, LLC v. Director of Revenue (2020) illustrates what can happen when records are incomplete. SEBA operated a donut shop called Eddie’s South Town Donuts in St. Louis. During an audit covering October 2011 through September 2014, the DOR requested business records, including sales journals, sales invoices, exemption certificates, and bank statements.
However, SEBA provided only partial records—no sales journals or invoices were produced. When the auditor requested that SEBA retain individual cash register receipts, the business provided only partial receipts and ultimately failed to maintain proper records.
The auditor concluded that SEBA had underreported its taxable sales by $400,483.72 and had failed to pay $23,431.89 in sales tax. The Administrative Hearing Commission ultimately found SEBA liable for $38,540.44 in unpaid sales tax, plus additions and statutory interest.
This case demonstrates how incomplete recordkeeping can lead to substantial assessments and how difficult it becomes to challenge an auditor’s findings without proper documentation.
Step 3: Understand the Audit Process
The Missouri sales tax audit typically follows a structured path. It all begins with the audit notice, after which the auditor will examine your records. On average, an auditor spends approximately one week examining records for a sales and use tax audit of a medium-sized company.
Audits are normally conducted at your business site, although other options such as off-site audits using electronic data or meetings at your tax professional’s office may be available. The auditor will examine your federal income tax return to reconcile gross sales between your federal return, sales tax return, and accounting records.
At the conclusion of the audit, the auditor will issue a Letter of Findings proposing any adjustments. This is not the final word; you have rights and options at this stage.
Example: The All-Star Amusement Exemption Certificate Case
In All Star Amusement, Inc. v. Director of Revenue (1994), the company operated cigarette, snack, and soda vending machines in the Kansas City metropolitan area. The director of revenue conducted a sales and use tax audit for the period January 1, 1985, through December 31, 1989. The audit was initially discontinued due to inadequate records and insufficient cooperation, then recommenced in November 1989.
At the administrative hearing, All Star presented signed exemption certificates from purchasers. However, some certificates were undated, and others were dated after the alleged exempt sales had occurred. The Administrative Hearing Commission held that sellers must receive exemption certificates contemporaneously with the sale. As a result, the AHC refused to find any sales made to buyers that had given undated exemption certificates.
This case highlights a critical lesson: exemption certificates must be properly completed, dated, and obtained at the time of sale. Failing to do so can result in the disallowance of exempt sales and a significant tax assessment.
Step 4: Consider Professional Audit Representation
While it is not strictly necessary to have an attorney present during an audit, having experienced audit representation can be invaluable. Navigating MO sales and use tax law is complex, and the stakes are high. A tax assessment from an audit can be challenging to negotiate.
The attorneys at Brydon, Swearengen & England P.C. specialize in sales and use tax litigation in Missouri. With decades of cumulative litigation experience and a solid understanding of the Missouri tax code, they assist businesses in resolving and litigating sales, use, and withholding tax issues.
From administrative hearings before the Missouri Administrative Hearing Commission (AHC) to appeals directly to the Missouri Supreme Court, having skilled legal counsel can significantly impact the outcome of your case.
Example: The Excel Drug Fraud Penalty Case
The case of Excel Drug Co. v. Missouri Department of Revenue (1980) demonstrates the severe consequences that can arise without proper representation and accurate recordkeeping. An investigation by the Special Investigation Bureau of the Department of Revenue examined Excel Drug’s books for the period January 1970 through March 1973.
The company’s president, who prepared the sales tax returns, admitted to investigators that the gross sales amounts shown on the returns were “pulled out of his head.” The audit found that Excel Drug had reported gross sales of just $179,317.32 when the actual gross sales were $743,198.07, a discrepancy of over $563,000. As a result, the director assessed additional state sales tax of $16,202.92, interest of $15,363.50, local taxes and interest, and, crucially, a 25% fraud penalty of $4,479.18 for a total assessment of $39,031.35.
This case illustrates how making up numbers on tax returns can trigger not only back taxes and interest but also fraud penalties that can devastate a business.
Step 5: Know Your Appeal Rights
If you receive an unfavorable assessment, you have the right to appeal. You must file a written petition for review with the Missouri Administrative Hearing Commission within 60 days of the assessment. This is a critical stage where presenting a well-organized case can lead to a settlement or a favorable resolution.
Key defense strategies include the following:
- Challenging the auditor’s methodology. Auditors sometimes use sampling and extrapolation to estimate liability; challenging the validity of their sample can reduce an assessment.
- Negotiating settlements. The most cost-effective solution is often negotiating a settlement with the DOR, potentially reducing overall liability.
- Understanding the law. Successful defenses are built on the precise interpretation of Missouri statutes and case law.
Example: The Consumer Contact Case. A Successful Appeal
Not all audit assessments withstand appeal. In Consumer Contact Co. v. State Department of Revenue, the company sold small desk items like desk pads, pen sets, calendars, and clocks. An auditor performed a sales and use tax audit for the period from January 1, 1974, to December 31, 1975. The audit revealed that Consumer Contact had collected and remitted state sales taxes on $987,707.00 in sales but had failed to collect taxes on an additional $20,411.00 in taxable sales. The auditor calculated that the company owed $612.33 in state sales taxes plus $151.59 in interest.
However, the audit also alleged that Consumer Contact owed $9,418.12 in Kirkwood City sales taxes and $4,709.07 in St. Louis County transportation sales taxes, amounts the company disputed. On appeal, the Missouri Supreme Court found that the Department’s determination was not supported by competent and substantial evidence and reversed the assessment.
This case demonstrates that audit assessments can be successfully challenged, but only with a well-prepared appeal and a clear understanding of the law.

Conclusion
Receiving a sales tax audit notice from the Missouri Department of Revenue is a serious matter, but it does not have to be a financial disaster. By carefully reviewing the notice, gathering comprehensive records, understanding the audit process, and seeking professional audit representation, you can navigate this challenge with confidence.
The real-world cases discussed above, from the SEBA donut shop’s recordkeeping failures to All Star Amusement’s improper exemption certificates, Excel Drug’s fraud penalty, and Consumer Contact’s successful appeal, all illustrate the importance of preparation, documentation, and legal guidance when facing a Missouri sales tax audit.
If you are facing a Missouri sales tax audit or have received a notice of assessment, don’t face it alone. Contact the experienced team at Brydon, Swearengen & England P.C. to protect your business’s interests.
FAQs
1. How long does a Missouri sales tax audit typically take?
On average, an auditor spends about one week examining records for a sales and use tax audit of a medium-sized company. However, the total duration depends on factors such as business size, industry type, and the complexity of accounting records.
2. What happens if I disagree with the auditor’s findings?
You have the right to appeal. You must file a written petition for review with the Missouri Administrative Hearing Commission within 60 days of the assessment. An unfavorable AHC decision can be appealed to the Missouri Supreme Court. As seen in the consumer contact case, some assessments are successfully reversed on appeal when the department’s evidence is insufficient.
3. Do I need an attorney to represent me during a Missouri sales tax audit?
While not required, having experienced legal representation is highly recommended. A skilled attorney can help negotiate with the DOR, challenge the auditor’s methodology, and ensure your rights are protected throughout the process. The Excel Drug case shows how devastating fraud penalties can be when businesses lack proper guidance.
4. How far back can the Missouri DOR audit my sales tax returns?
Missouri law requires records to be kept for at least three years. However, if the DOR discovers fraud or significant income understatements, it may go back further. The DOR recommends retaining records for five years. The Excel Drug audit covered a period from 1970 through 1973, demonstrating that audits can reach back multiple years when issues are identified.
5. What types of records will the auditor request?
The auditor will typically request copies of sales and use tax returns, sales journals, general ledgers, invoices, bank statements, and exemption certificates. As the All-Star Amusement case demonstrates, exemption certificates must be properly dated and obtained contemporaneously with the sale. If your records are electronic, providing them through the DOR’s CAAP program can expedite the process.