In this study, a relatively effective process is used to sterilize Escherichia coli on the surface of micro-sized calcium citrate powder using nitrogen and argon as process gases in a low-temperature vacuum plasma treatment. The purpose of this study is to confirm and to introduce the effectiveness of homogeneous surface treatment for the sterilization of fine inorganic powder by the rotatable low-temperature RF plasma system designed by ourselves. The results of the test using 3M petrifilm showed that there were no remarkable spots in the case of the surface of plasma treated powder, whereas the untreated powder showed many blue spots, which indicating that the E. coli was alive. After 5 days, in the same samples, the blue spots were seen to be larger and darker than before, while the plasma-treated powder showed no changes. The results from FE-SEM analysis showed that the E. coli was damaged and/or destroyed by reactive species generated in the plasma space, resulting in the E. coli being sterilized. Furthermore, the sterilization effects according to the selected parameters (N2 and Ar; flow rate 30 and 50 sccm) adapted in this study were mutually similar, regardless of such different process parameters, and this indicates that homogeneous treatment of powder surfaces could be more effective than conventional methods. Therefore, the plasma apparatus used in this study may be a practical method to use in a powerful sterilization process in powder-type food.