In this paper, the underwater performance of atmospheric-pressure plasma jets with and without a porous dielectric material is compared. The comparison included a multi-channel discharge plasma jet with a porous dielectric that served to generate microdischarges in the dielectric and thereby increased the plasma density, and a single-discharge jet of a typical pen-type atmospheric pressure plasma jet without a porous dielectric. In the analysis, the electrical and optical characteristics, concentration of reactive chemical species, and underwater sterilization performance were characterized. The multi-channel discharge plasma jet was found to effectively sterilize over 99.9% of the Escherichia coli. The decimal reduction times of the single- and multi-jets were 13.13 and 6.98 min, respectively, due to their physical and chemical properties. The results confirmed that the sterilization rate of the multi-channel discharge plasma jet was 1.88 times faster than that of the single-discharge jet.