Background: Medical equipment must be thoroughly sterilized before use. A potentially useful method for sterilizing medical equipment is non-thermal atmospheric pressure plasma technology. Plasma can be applied directly using cold atmospheric pressure plasma jet (CAPPJ) or indirectly using a plasma-activated mist (PAMi). Aim was to assess the bactericidal effect of direct plasma (CAPPJ) and indirect plasma (PAMi) as new methods of sterilizing stainless steel compared to autoclaving, which is considered the gold standard for sterilizing heat-stable material. Method: This comparative experimental study included 36 E. coli and 30 S. aureus, strains which were isolated from various clinical specimens and identified by conventional methods. They were exposed to three different treatment methods: direct CAPPJ, indirect PAMi, and autoclaving. The time needed to reach medical sterility assurance level (SAL) was recorded for each method. Results: There was high statistically significant difference between E. coli and S. aureus bacterial counts using direct and indirect plasma at different exposure time intervals. There was a high statistically significant relation between decreasing bacterial counts and the exposure to direct plasma, indirect plasma and autoclave at different time intervals. The shortest time needed to reach SAL was recorded for direct plasma as 1.9 and 3.1 minutes for E. coli and S. aureus, respectively. Conclusion: CAPPJ and PAMi are rapid effective methods not only in eradication of the tested E.coli and S.aureus isolates but also in reaching SAL for stainless-steal medical instruments. These promising methods can save long time consumed by conventional methods for sterilization especially in emergencies.