The nexus of quantum information science and chemistry is rapidly developing. In our lab we have found it fruitful to view the microscopy of molecules as an exercise in quantum metrology, even under seemingly “messy” conditions. I will discuss how this line of thought has led us to establish fundamental error bounds for microscopy tasks including the resolution of fluorophore lifetime mixtures and the discrimination of enantiomers by their chiroptical emission. In particular, I will discuss our lab’s recent experimental demonstration of a passive, “quantum-inspired” approach to super-resolution microscopy, circumventing “Rayleigh’s Curse” without requiring active control of fluorescent labels. Finally, I will discuss how we’ve repurposed common organic dyes as photoswitchable spin qubits for nanoscale magnetic resonance studies by interfacing them with single, shallow nitrogen-vacancy centers in diamond.