Most photosensitizers are derived from bulky fluorescent scaffolds, which impair their active uptake as photosensitive metabolites. Smaller fluorophores, such as pyrroloindolizines, nitrobenzodiazoles and naphthylamines, are more appropriate to retain metabolite function. In this work, we have designed a platform based on amino-substituted benzoselenadiazoles as the smallest photosensitizers reported to date and used them to build photodynamic agents that recapitulate the uptake of native metabolites, unlike some commercial photosensitizers. Benzoselenadiazole probes can selectively kill cells exhibiting altered metabolism with high spatial resolution and only after exposure to non-toxic light. Importantly, we demonstrate that benzoselenadiazoles are compatible with different metabolite structures (e.g., amino acids, saccharides) and can be used to ablate a variety of disease-causing cells, from bacterial pathogens in vitro to glioblastoma microtumors in vivo. This new chemical platform demonstrates how small photosensitizers can harness early metabolic signatures to safely eliminate harmful cells in vivo without damaging healthy tissues.