Carbon‐based nanomaterials have demonstrated to be potent candidates for biomedical applications. Recently, graphene quantum dots (GQDs) have emerged as an attractive tool for bioimaging, biosensing, and therapy. Hence, studying their biodegradability in living systems is essential to speed up the translation toward real clinical innovations. Here, the enzymatic degradation of GQDs using human myeloperoxidase and eosinophil peroxidase is investigated. Transmission electron microscopy, fluorescence, and Raman spectroscopy are used to evaluate the biodegradation of GQDs. Signs of degradation by both enzymes are observed already after a few hours of incubation with each enzyme, being more evident after a couple of days of treatment. Molecular dynamics simulations show intimate interactions between the enzymes and the GQDs. The conformation of both peroxidases is slightly altered to favor the interactions, while the GQD sheets distort a little to adapt to the surface of the enzymes. The biodegradability of the GQDs ensures their real potential in the practical biomedical applications.