Aggregation of proteins is involved in many disorders. Besides amyloid fibrils, which mostly form in the brain, other kind of protein aggregates can lead, for example, to clots in the blood or floaters in the vitreous of the eye. This review is not only limited to amyloid diseases but aims at giving the reader a general overview on how nanomaterials can be employed to avoid and destroy protein aggregates of different nature. Thanks to their recognized versatility, nanomaterials may offer attractive features against harmful protein aggregates. In addition to their known ability to interact with proteins, we also aim at providing a state-of-the-art on how stimuli-responsive nanomaterials can be employed to destroy aggregates. Despite promising and conceptually interesting strategies on how nanomaterials can lead to the destruction of protein aggregates and the prevention of their formation, it appears clearly that many efforts still remain, however, to demonstrate in vivo feasibility and safety to pave the way for clinically relevant therapies.