A number of rapid microbiological methods capable of aerosol-based microbial detection are quickly emerging for use in the pharmaceutical and food markets. A subset of these technologies utilizes intrinsic microbial fluorescence as the basis for bioaerosol detection. This fundamental method of detection is relatively new to the pharmaceutical and food industries, which rely on traditional culture-based methods implemented decades ago to gain an understanding of their manufacturing environments. When combined with real time and continuous assessment, intrinsic fluorescence-based detection provides a new level of information and monitoring in these environments. One aspect of this monitoring relates to the detection of stressed micro-organisms. Bacteria found in pharmaceutical and food manufacturing environments can be in a stressed state due to heat, UV, or chemical exposure, desiccation, and so forth. As a result, the ability of an environmental monitoring system to detect stressed microbes is of particular interest. A commercially available, intrinsic fluorescence-based bioaerosol detection RMM was utilized in this study to determine the ability of such systems in the detection of heat-stressed microorganisms. An assessment of culturability and growth delay in control and heat-stressed samples was performed to confirm stress. Furthermore, the performance of the intrinsic fluorescence-based bioaerosol detection systems were compared to the SAS Super 100, MAS-100 NT, and SMA air samplers in the detection of heat-stressed Escherichia coli, Staphylococcus epidermidis, and Bacillus atrophaeus spores. These bacteria were selected because they are industry-relevant organisms, commonly found in various manufacturing environments, that represent a Gram-positive, Gram-negative, and spore-forming bacteria, respectively. It was found that the intrinsic fluorescence-based bioaerosol detection systems can detect heat-stressed microorganisms, including those that are not detected by the traditional culture-based method due to the inability of the stressed microbes to form colony-forming units.