Individual-based microbial ecology (IBME) is a developing field of study in need of experimental tools to quantify the individual experience and performance of microorganisms in their natural habitats. We describe here the conception and application of a single-cell bioreporter approach with broad utility in IBME. It is based on the dilution of stable green fluorescent protein (GFP) in dividing bacteria. In the absence of de novo synthesis, GFP fluorescence of a daughter cell approximates half of that of its mother, from which follows that the fluorescence of a progeny cell is a quantitative measure for the reproductive success of its ancestor. To test this concept, we exposed GFP-filled bacteria to different degrees of environmental heterogeneity and assessed how this affected individual cells by the analysis of GFP content in their progeny. Reporter bacteria growing in rich medium in a shaking flask showed no variation in reproductive success, confirming that life in a broth is experienced much the same from one bacterium to the next. In contrast, when reporter bacteria were released onto plant leaf surfaces, representing a microscopically heterogeneous environment, clear intrapopulation differences in reproductive success were observed. Such variation suggests that individual cells in the founding population experienced different growth-permitting conditions, resulting in unequal contributions of individual bacteria to future offspring and population sizes. Being able to assess population changes bottom-up rather than top-down, the bioreporter offers opportunities to quantify single-cell competitive and facilitative interactions, assess the role of chance events in individual survivorship and reveal causes that underlie individual-based environmental heterogeneity.