A water-assisted microwave treatment was studied against the pathogenic bacterium Salmonella Typhimurium in fresh jalapeño peppers and coriander foliage. Vegetables were immersed in water and treated in a microwave oven at 950 W to reach up 63 °C: jalapeño pepper for 25 s and coriander foliage for 10 s. After the microwave heating, samples were cooled in water at 4 °C. Samples were observed with confocal microscope before and after treatment. The proposed protocols resulted in a reduction of 4–5 log cycles on the Salmonella population, which is the main issue from the microbiological viewpoint. Even color of the vegetables was affected by the treatments (p < 0.05) mainly by darkening in both vegetables and loss of greenness in jalapeño pepper, no changes in firmness were observed. Sensory acceptance of a salsa formulated with the treated vegetables had high scores (7.21 in a 9-points hedonic scale).