Cold plasma as a promising method to boost food safety and improve shelf life has triggered a huge amount of innovative scientific inquiry. The current study evaluates the effect of air plasma surface barrier discharge (SBD) treatment on the inactivation of Aspergillus niger spores for saffron stigma post packaging. The induced effects of the process on the physicochemical properties of the product are assessed. To identify the decontamination agents and plasma-produced reactive oxygen and nitrogen species, optical emission spectroscopy, ozone, and NOx measurements were used. The influence of plasma treatment on the surface morphology, antioxidant activity, color, flavor, odor, nitrate, and ammonium content of samples was determined by field emission scanning electron microscopy (FESEM), 2,2-diphenyl-1-picrylhydrazyl (DPPH), ultraviolet-visible spectrophotometry, colorimetry, high-performance liquid chromatography (HPLC), and ion chromatography (IC), respectively. The results showed that increased treatment time increased the germination period for Aspergillus niger conidia with spore growth ceasing after 2 min of plasma exposure. The antioxidant inhibition percentage of control and 2-min plasma-treated samples was 23.386 and 25.861, respectively. FESEM images showed this remote plasma treatment method did not etch the cell wall of saffron strands. The results of HPLC and IC analysis indicated that plasma treatment had no obvious effect on the main chemical compounds of saffron. The findings point to the potential of SBD plasma processing for packaged saffron with no detrimental effects on the vital components responsible for odor, flavor, color, antioxidant activity, and morphology. The SBD plasma offers a rapid and low-cost solution for saffron sanitization.