This study investigated the relationship between bacterial counts and volatile organic compound (VOC) formation in 3.9% fat milk. The milk was stored at 7, 10, 13, 15 and 19 (±1 °C). Volatile compounds were measured using solid‐phase microextraction with gas chromatography. Enzyme activity was also monitored throughout the shelf life. Results show that volatile organic compound concentrations increased with higher bacterial counts (5.0–7.0 log10 cfu/mL). Bacterial counts correlated closely with acetaldehyde, butanone, ethanol, hexanal, acetone and fatty acid concentrations. Results indicate that protease and lipase activities increased and correlated closely with VOCs. Formation of VOCs was detectable when protease and lipase activities reached 1.2–1.3 U/mL and 0.32–0.350 meq/mL, respectively. These findings provide a basis for the monitoring of milk quality using chemical sensors that are sensitive to VOCs, particularly under conditions of thermal abuse.