Background: Cooking activities generate pollutants that can cause adverse health effects to occupants. This study aims to characterize the indoor air environment in small and medium food enterprises (SMEs), as studies in this area are scarce. Methods: A series of field measurements were conducted to investigate the IAQ at 14 SMEs selected in Pulau Pinang for three different cooking methods (frying, boiling, and baking). Data on environmental perception and health symptoms were obtained from 76 workers by using a validated questionnaire. Boosted regression tree (BRT) analysis and parametric tests were performed to evaluate the impact of the IAQ on the prevalence of disease symptoms. Results: The results showed that CO2, temperature, and relative humidity were higher than the standard limits, while PM2.5 and TVOC were below the standard limits. Using BRT analysis, CO2 was indicated as the highest pollutant to cause complaints by workers (41.55%), followed by CO (21.93%), relative humidity (11.81%), temperature (10.66%), PM2.5 (7.07%), and TVOC (6.99%). This study indicated that workers in SMEs food industries are affected by the indoor air quality at their workplace in which CO2 was the main parameter influencing their health. This study suggests that future research focuses on boiling and frying SMEs with CO2, CO, temperature, and relative humidity to be afforded emphasis.