Streptococcus pneumoniae (the pneumococcus) is the world’s foremost bacterial pathogen and is responsible for more than one million deaths globally every year. As a host-adapted pathogen, the pneumococcus has developed complex mechanisms to subvert the antimicrobial changes in the elemental chemistry of host niches during infection. Depending on the host niche and stage of infection, the innate immune response can utilise either metal ion withholding strategies to starve the pneumococcus of essential trace elements or increase their relative abundance to intoxicate the pathogen. The temporal and spatial changes in host niche elemental abundance necessitate further investigation to understand the complexity of innate immune antimicrobial strategies. To address this question, we have generated S. pneumoniae strains with chromosomally integrated fluorescent reporters responsive to the major in vivo elemental changes, namely manganese starvation, copper intoxication and zinc intoxication. To quantify bacterial stress responses, we have developed a plate-based fluorescence polarisation assay. Here, we demonstrate the application of these reporter strains in the presence of extracellular metal ion stress. Our work shows that metal stress corresponds proportionally with the fluorescence output. By comparison with absorbance-based bacterial viability measurements, fluorescence polarisation is a demonstrably more comprehensive tool to assess dynamic cellular responses to stress. Collectively, this work reports the development of a fluorescent reporter system and associated assay that provides a highly useful tool for further investigation of bacterial pathogenesis and the interplay between host and pneumococcus.