The large number of deaths induced by carcinoma and infections indicates that the need for new, better, targeted therapy is higher than ever. Apart from classical treatments and medication, photodynamic therapy (PDT) is one of the possible approaches to cure these clinical conditions. This strategy offers several advantages, such as lower toxicity, selective treatment, faster recovery time, avoidance of systemic toxic effects, and others. Unfortunately, there is a small number of agents that are approved for usage in clinical PDT. Novel, efficient, biocompatible PDT agents are, thus, highly desired. One of the most promising candidates is represented by the broad family of carbon-based quantum dots, such as graphene quantum dots (GQDs), carbon quantum dots (CQDs), carbon nanodots (CNDs), and carbonized polymer dots (CPDs). In this review paper, these new smart nanomaterials are discussed as potential PDT agents, detailing their toxicity in the dark, and when they are exposed to light, as well as their effects on carcinoma and bacterial cells. The photoinduced effects of carbon-based quantum dots on bacteria and viruses are particularly interesting, since dots usually generate several highly toxic reactive oxygen species under blue light. These species are acting as bombs on pathogen cells, causing various devastating and toxic effects on those targets.