Micro capsulation is an essential technique to stabilise and protect active ingredients of nutraceuticals during various manufacturing processes. This study aimed to control bacterial contamination of nutraceutical raw materials and protection of nutraceutical active ingredients using chitosan microcapsules. Thirteen bacterial isolates were isolated from ginger GI and garlic G. Thermal resistance isolates (GI 7, GI 3& G2) were exposed to different gamma radiation doses; their lethal doses were 8.0 KGy for GI 3, and 9.0 KGy for G 2 and GI 7. The GI 3 and GI 7 isolates showed relative resistance against chitosan, they were identified by 16S rRNA gene sequencing as Enterococcus faceium and Enterococcus durans, respectively. A microcapsule preparation was formed using the emulsion cross-linking method by incorporating ginger or garlic with chitosan. The results revealed that the chitosan concentration of 4% and 20 ml of GST achieved 92.5% and 87.5% encapsulation yields for chitosan/ginger and chitosan/garlic microcapsules, respectively. Chitosan-ginger formed microcapsules were thermally stable while Chitosan-garlic microcapsules were partially unstable.