Mycotoxins are natural secondary metabolites of fungi occurring in foods which can cause adverse health effects. Contamination of foods with microorganisms and mycotoxins can occur at various stages along the value chain, and spices are not exception. Red pepper (Capsicum annuum L.) is one of the major spices consumed globally, recognized for its distinctive aroma, color, pungency and nutritional value. It also significantly contributes to the national economy for high producing countries like Ethiopia. However, natural contamination and occurrence of fungi with subsequent production of aflatoxins (AFs), ochratoxin A (OTA) and other mycotoxins in red pepper have posed a serious concern in the food system. Though mycotoxin contamination of red pepper has been evidently studied and well documented, studies regarding efficient decontamination techniques are scant. Therefore, this study aimed to investigate the impact of selected emerging food processing technologies (electron beam (e-beam), pulsed light (PL) and high pressure processing (HPP)) on the decontamination of naturally occurring microorganisms and mycotoxins in red pepper. Initially, the physicochemical, functional, thermal, oxidative stability and rheological properties of red pepper powder and paste were characterized. The compositional analysis showed that the red pepper powder contained 14.50, 44.00 and 7.57 g/100 g of crude fat, crude fiber and ash, respectively. The concentration of total phenols (TP), carotenoids and antioxidants activity of the powder were 1.04 g GAE/100 g, 374 mg ï¢c/100 g and 38.61 μmol TE/g, respectively. Findings on functional properties revealed that the bulk and tapped density were 395.1 kg/m3 and 583.4 kg/m3, respectively, indicating higher compressibility of the powder. In contrast, Hausner ratio (1.48), Carr‘s index (32%) and angle of repose (45°) indicated poor flowability of the powder. Particle size distribution also indicated that the volume weighted mean values D[4,3] of the powder and paste were 262.20 and 201.46, respectively. Emulsifying, oil and water absorption capacities of the powder were 47.5%, (1.41 to 1.73) g/g and (0.86 to 2.29) g/g, respectively. Higher glass transition temperature was observed for the powder (62.54 °C) than the paste (45.64 °C). The induction period indicated that red pepper was more stable against oxidation in powder form (5.2 h) than in paste (3.2 h). Rheological analysis revealed that the paste exhibited shear-thinning behavior at 25 °C. As aforestated, red pepper is an important spice with vital nutritional composition and techno-functional properties, and with immense potential for industrial application and product development. However, in recent years, frequent contamination with fungi and mycotoxins posed health concerns and hampering the export market. Thus, investigations on efficient decontamination techniques are critical. The first evaluated treatment was e-beam with variable doses of up to 30 kGy. Significant (P0.95). With the lowest fluence (1.0 J/cm2), carotenoids and antioxidants activity reduced significantly (P