Carbon nanotubes (CNTs) have emerged as a leading nanomaterial for biomedical applications because of their extraordinary properties, which make them useful as delivery vehicles for drugs, proteins, and DNA into cells. However, the numerous applications of carbon nanotubes inevitably increase the potential risk of this nanomaterial. To address this issue, it is necessary to develop protocols for the effective and safe degradation of CNTs. In this study, we demonstrate a self-degradation route for single-wall carbon nanotubes mediated by the built-in peroxidase-like activity of bacterial magnetic nanoparticles (BMPs). Biocompatible BMPs which originated from Magnetospirillum sp. AMB-1 were directly conjugated through covalent bonding to functionalized SWNTs (f-SWNTs) without any additional functionalization processes. This SWNT–BMP hybrid was proven to exhibit highly synergetic peroxidase-like activity, and BMPs act as a highly effective intrinsic peroxidase for the self-degradation of BMP-decorated SWNTs. Moreover, it was shown to be an inhibitor that reduces the formation of β-amyloid (Aβ) fibrils, which are considered a key element in Alzheimer's disease. Thereby the SWNT–BMP hybrid exerts neuroprotective effects against β-amyloid (Aβ) fibrillation-induced neurotoxicity in SH-SY5Y human neuroblastoma cells. These results suggest that the SWNT–BMP hybrid could offer a new approach for treating or preventing neurodegenerative diseases.