No, paying by cash does not initiate any special investigations by the IRS.
The IRS treats payments by cash the same as those made by other payment methods. All taxpayers, whether individuals or businesses, are required to pay federal taxes regardless of the payment method used. The IRS does not differentiate between cash payments and other forms of payment in terms of initiating investigations.
Sources:
Publication 1544 (9/2014)
Instructions for Form 8300 (12/2023)
§ 6050I. Returns relating to cash received in trade or business, etc.
IRM Part 9. Criminal Investigation. Chapter 5. Investigative Process. Section 5. Money Laundering and Currency Crimes
FS-2021-3
IRM Part 4. Examining Process. Chapter 26. Bank Secrecy Act. Section 10. Form 8300 History and Law