Maintaining single-walled carbon nanotubes in their pristine state (i.e. devoid of aggregation and inhomogeneous doping) within nanostructured photovoltaic devices is a major challenge.  In this contribution, we report on the synthesis and self-assembly of a C₆₀-functionalized flavin (FC₆₀), composed of PCBM and isoalloxazine moieties attached on either ends of a linear aliphatic spacer.  Small amounts of FC₆₀ (up to 3 molar %) were shown to co-assembly with an organic soluble derivative of flavin (FC12) around SWNTs and impart effective dispersion and individualization.  Steady state and transient absorption spectroscopy illustrate that 1% or higher incorporation of FC₆₀ allows for an effective photo-induced charge transfer quenching of the encased SWNTs through the seamless helical encase.  This is enabled via the direct π-π overlap between the graphene sidewalls, isoalloxazine helix and the C₆₀ cage, that facilitates SWNT exciton dissociation and electron transfer to the PCBM moiety.  Atomistic molecular simulations elucidate how the fullerene is brought in the vicinity of the isoalloxazine helix to quench the nanotube.  The narrow E^S_ii linewidth for the resulting ground state complex indicates a new class of highly organized supramolecular nanotube architecture with profound importance for advanced nanostructured devices.