Although graphene-based materials continuously expand their range of industrial and biomedical applications, understanding their long-term fate in the organisms and environment is still in its infancy. Herein we examine the biodegradation of partially reduced graphene oxide (p-rGOn) and magnetic nanoparticles (IONP) adsorbed p-rGOn (@rGOn) by incubating with the human myeloperoxidase (hMPO) isolated from the neutrophils, including with plant enzyme, horseradish peroxidase and treating with microbial laccase in the presence of its redox mediator ABTS [2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)]. Further, the biodegradation of p-rGOn and @rGOn was investigated by incubating with the laccase-secreting fungi, Aspergillus sp., present in the compost soil. The biodegradation of both p-rGOn and @rGOn samples was analyzed for morphological and structural changes using electron microscopy and Raman spectroscopy. The results confirmed the efficient degradation of p-rGOn and that the presence of IONP enhanced the biodegradability of @rGOn (magnetic) over p-rGOn, which could be attributed to the Fenton-type reaction because of IONP. These results confirmed that the presence of IONP facilitates the magnetic manipulation of @rGOn and increases their biodegradability. The current work could be crucial for better designing the potential biomedical applications of @rGOn (magnetic) for near-infrared photothermal (PTT) and externally controlled magnetotherapy applications useful in cancer treatment.