Chocolate milk typically has higher microbiological counts than unflavored milk and is susceptible to off-flavor development before the end of targeted shelf life. It has been suggested that the addition of multiple ingredients (chocolate, sucrose, stabilizers, and vitamin A and D) contributes to expedited growth of spoilage organisms in chocolate milk. The objective of this study was to isolate and identify the organisms responsible for off-flavor development in nonfat chocolate milk. Nonfat chocolate milk was obtained from regional fluid milk processors (3 plants). At the end of shelf life (18 d) off-odors had developed and the milk was serial diluted and spread plated on standard and differential media including tryptic soy agar, De Man, Rogosa and Sharpe agar, skim milk agar, spirit blue agar, chocolate milk agar, and MacConkey agar. Isolates were streaked on chocolate milk agar (standard methods agar with 10% vol/vol chocolate milk). Five causative isolates were selected based on the development of off odors (band-aid, fishy, and bready) after growing on chocolate milk agar. Selected isolates were inoculated in triplicate at varying levels (1–4 log cfu/mL) into UHT nonfat chocolate milk to confirm off-odor development. Off-odors developed after 5–14 d with 7°C storage. Whole genome sequencing was performed on isolates and species were determined by 16S rRNA and rpoB sequence comparisons in the NCBI database. “Band-aid” odor was associated with Psychrobacillus psychrotolerans, bready odor with Paenibacillus odorifer, and fishy odor with Acinetobacter guillouiae. Knowing the identification of these spoilage organisms in chocolate milk can help fluid milk processors monitor for these microorganisms. Determining their prevalence and point of entry can help control the risk of an off-flavor spoilage event through targeted processing parameters and sanitation methods.