There is a strong and ever-escalating need for sterilization tools that are effective against a broad range of pathogenic microorganisms. To address this issue, this study evaluates the inactivation potential of arc and pulsed spark plasma discharges on Pseudomonas aeruginosa, Staphylococcus aureus, Microsporum canis, Trichophyton mentagrophytes, and Candida albicans microorganisms. Our results show that the electrical discharge plasma systems are effective in the inactivation of pathogenic microorganisms. The inactivation of the considered strains was greatly affected by the type of microorganisms. Higher viability losses of the pathogenic strains were observed in bacterial strains than in the fungal strains. Moreover, in the case of fungal strains, the population of C. albicans was decreased the most, followed by Trichophyton mentagrophyte, while the population of Microsporum canis was decreased the least. Besides, the arc discharge system was compared with the pulsed spark discharge system. It can be obtained from the results that the pulsed spark discharge treatment successfully enhanced the reduction of the pathogenic cells more than the arc discharge treatment. The higher efficiency of the pulsed spark discharge is due to the generation of discharge streamers on the water surface. The SEM analyses showed that electrical discharge plasmas produced serious damage to pathogenic eukaryotic and prokaryotic microorganisms. Also, the plasma-induced changes in pH values and temperature values were measured. The pulsed spark discharge-treated samples have more significant changes in pH value while arc discharge-treated samples have larger temperature changes.