Pulsed light plasma (PLP) treatment was developed as a simultaneous treatment with cold plasma (CP) and intense pulsed light (IPL) to inactivate Aspergillus flavus spores, Bacillus pumilus spores, and Escherichia coli O157:H7 in red pepper flakes. PLP treatment non-thermally inactivated A. flavus spores, B. pumilus spores, and E. coli O157:H7 by 1.3 ± 0.1 log spores/g, 2.3 ± 0.2 log spores/g, and >3.8 log CFU/g Est. (estimated based on the number of survivors with counts below 20 on agar plates), respectively. PLP treatment did not alter the color and moisture content of the red pepper flakes. PLP treatment caused cell membrane degradation in A. flavus spores, B. pumilus spores, and E. coli O157:H7, as well as DNA damage to B. pumilus spores and E. coli O157:H7. The microbial inactivation efficacy of consecutive treatments with CP and IPL did not differ from that of PLP. Moreover, the inactivation efficacy was higher in flakes at aw 0.73 than at 0.57. The results of this study suggest that PLP treatment is a feasible non-thermal technology for decontaminating red pepper flakes.