Nuts a great source of vital vitamins, minerals and bioactive substances, and their consumption is increasing globally. In the present study, Walnut, Cashew and Almond samples were collected from local market of District Islamabad to optimize bacterial isolation protocol and use the cold plasma technique to reduces these pathogens from the surface of nuts. Bacteria were characterized by colony morphology/shape, biochemical tests and Gram. Six bacterial species were identified through gram staining and by chemical testing. All the nut (walnut, cashew and almond) samples were treated with Surfaguide microwave (MW) plasma device for 10, 15, 30 second and for 1 to 2 minutes. The gas flow rate range was (1.5-1.7 SCCM), plasma generating power (0.38,0.7,1.21 kW) and treatment time was 15s-2min. Among all of these three samples, after the treatment shown the reduction of bacterial colonies. After 10 and 15s treatment time, minimal bacterial reduction rate was observed in the three tested nut samples. At 30s treatment time walnut sample, almond samples, and cashew samples showed 4.36 log reduction, 1.70 log reduction, and 1.81 log reduction respectively. Scanning electron microscopy (SEM) was used to check the surface morphology of nuts. Thirty seconds treatment of non-thermal plasma (NTP) did not affect nuts morphology, and one-minute NTP treatment affected the nut samples morphology. This study proved that Surfaguide Cold Plasma efficiently reduces surface bacterial count on walnut, almond and cashew at 30 seconds NTP treatment time without effecting nuts physical morphology.