The Cold Plasma (CP) treatment efficiency to inactivate naturally fungi contaminated beans (Phaseolus vulgaris L.), Class black, and the effects in micro-structures stability were investigated. Kernels were exposed to CP (8 kv intensity and 510W power) at different times (5, 10, 20 and 30 min) followed by incubation to verify the antifungal effect and their micro-structural resistance through microscopy (stereo –SM and scanning electron - SEM) observation. The treatment was effective to fungal inactivation when exposed to CP (10-30 min). It also inhibited bean germination during the longest treatment exposure (20-30 min). Regarding germination, only when CP was applied during the shortest period of time (5 min) had a positive effect (improved its speed: hypocotyl & radicle length increased), when compared to Control. Some morphological alterations were registered by SM, either on testae (wrinkling) and cotyledons (color changes). Indeed, through SEM, both testae and cotyledon structures showed the disrupting effects on their cell membranes during the treatment more power. The CP treatment, under the current conditions applied, showed effective for fungi inactivation, although it affected some kernel micro-structures and germination. Therefore, further studies will be carried out regarding adjustments on CP conditions, to improve treated beans quality.