Recent studies concerning graphene quantum dots (GQDs) focus extensively on their application in biomedicine, exploiting their modifiable optical properties and ability to complex with various molecules via π–π or covalent interactions. Among these nascent findings, the potential therapeutic efficacy of GQDs was reported against Parkinson’s disease, which has to date remained incurable. Herein, we present an environmentally friendly approach for synthesizing GQDs through a waste-to-treasure method, specifically from coffee waste to nanodrug. Consistent with the previous findings with carbon fiber-derived GQDs, the inhibitory effects of coffee bean-derived GQDs demonstrated similar effectiveness against abnormal α-synuclein fibrillation and the protection of neurons from relevant subcellular damages. The fact that a GQDs-based nanodrug can be prepared from a non-reusable yet edible source illustrates a potential approach to convert such waste materials into novel therapeutic agents with minimal psychological rejection by patients.