The study delved into the impact of two extrusion processing parameters—screw speed (SS at 400, 600, 800 RPM) and material moisture content in the extruder barrel (M at 12, 15, 18%) at constant feed rate (50 kg/h)—on reducing the content of alternariol (AOH), alternariol monomethyl ether (AME), tenuazonic acid (TeA), and tentoxin (TEN) in whole-grain red sorghum flour. Ultra-performance liquid chromatography coupled with a triple-quadrupole mass spectrometer (UPLC-MS/MS) was used for determination of Alternaria toxin levels. The extruder die temperature ranged between 136 and 177 °C, the pressure at the die was from 0.16 to 6.23 MPa, the specific mechanical energy ranged from 83.5 to 152.3 kWh/t, the torque ranged between 88 to 162.8 Nm, while the mean retention time of material in the barrel was between 5.6 and 13 s. Optimal parameters for reducing the concentration of all Alternaria toxins with the satisfactory quality of sorghum snacks were: SS=400 RPM, M= 12%, with a reduction of 61.4, 76.4, 12.1 and 50.8% for AOH, AME, TeA and TEN, respectively.