Aroma composition and microbial quality of identical lots of apple cider treated by pulsed electric field (PEF), ultraviolet irradiation (UV), or thermal pasteurization stored at 4 degrees C were compared at 0 and 4 weeks. Conditions were optimized to achieve identical 5 log reductions in Escherichia coli K12 for each treatment. PEF and thermal pasteurization maintained acceptable microbial quality for 4 weeks, but UV samples fermented after 2 weeks. Twenty-eight volatiles were quantified using gas chromatography-mass spectrometry (GC-MS) and odor activity values (OAV) determined. OAVs of 69:hexyl acetate, 41:hexanal, 25:2-methylbutyl acetate, 23:2-methyl ethyl butyrate, and 14:2-(E)-hexenal were observed for the control cider. Significant differences (p < 0.05) in the levels of these odorants were observed between treated apple ciders only after 4 weeks of storage. Thermal samples lost 30% of the major ester and aldehyde volatiles during storage with significant decreases (p < 0.05) in butyl acetate, 2-methylbutyl acetate, hexanal, and 2-(E)-hexenal. In UV cider, hexanal and 2-(E)-hexenal were completely lost after 4 weeks of storage. Microbial spoilage in UV cider after 4 weeks of storage was chemically confirmed by the detection of the microbial metabolite 1,3-pentadiene. PEF cider lost <2% of its total ester and aldehydes after 4 weeks of storage and was preferred by 91% of the sensory panel over thermally treated cider.