Carbon quantum dots (CQDs) have emerged as potential alternatives to classical metal-based semiconductor quantum dots (QDs) due to the abundance of their precursors, their ease of synthesis, high biocompatibility, low cost, and particularly their strong photoresponsiveness, tunability, and stability. Light is a versatile, tunable stimulus that can provide spatiotemporal control. Its interaction with CQDs elicits interesting responses such as wavelength-dependent optical emissions, charge/electron transfer, and heat generation, processes that are suitable for a range of photomediated bioapplications. The carbogenic core and surface characteristics of CQDs can be tuned through versatile engineering strategies to endow specific optical and physicochemical properties, while conjugation with specific moieties can enable the design of targeted probes. Fundamental approaches to tune the responses of CQDs to photo-interactions and the design of bionanoprobes are presented, which enable biomedical applications involving diagnostics and therapeutics. These strategies represent comprehensive platforms for engineering multifunctional probes for nanomedicine, and the design of QD probes with a range of metal-free and emerging 2D materials.