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The impact of pulsed light (PL) treatment on naturally occurring microorganisms, mycotoxins, and on physicochemical properties in red pepper powder was investigated. Powder samples were exposed to different PL treatments up to 61 pulses, with fluence ranging from 1.0 to 9.1 J/cm2. The highest fluence applied (9.1 J/cm2, 61 pulses, 20 s) resulted in 2.7, 3.1, and 4.1 log CFU/g reduction of yeasts, molds, and total plate counts (TPC), where initial microbial loads were 4.6, 5.5, and 6.5 log CFU/g, respectively. At the same fluence intensity, a maximum reduction of 67.2, 50.9, and 36.9% of aflatoxin B1 (AFB1), total aflatoxins (AF), and ochratoxin A (OTA) were detected, respectively. Proportional increase in temperature of the samples was observed from the absorbed PL energy, reaching maximum of 59.8°C. The inactivation of investigated microorganisms and mycotoxins followed first-order kinetics (R2 > 0.95). The fluence intensity at 6.9 and 9.1 J/cm2 did not cause degradation, but rather a significant (p < .05) and apparent increase of total phenols. Total color difference (ΔE*) revealed only “slight differences,” compared to the untreated sample. In conclusion, higher reduction of microbial load and mycotoxins in red pepper powder could be achieved, when higher treatment intensity was applied. This suggests the PL as a potential technology for decontamination of red pepper powder and other spice powders.