In this contribution, we describe the synthesis and covalent attachment of an analogue of the flavin mononucleotide (FMN) cofactor onto carboxylic functionalities of single-walled carbon nanotubes (SWNTs). The synthesis of FMN derivative (12) was possible by coupling flavin H-phosphonate (9) with an aliphatic alcohol, using a previously unreported N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride coupling. We found that the flavin moiety of 12-SWNT shows a strong pi-pi interaction with the nanotube side-walls. This leads to a collapsed FMN configuration that quenches flavin photoluminescence (PL). The treatment of 12-SWNT with sodium dodecyl sulfate (SDS) overcomes this strong nanotube/ isoalloxazine interaction and restores the FMN into extended conformation that recovers its luminescence. In addition, redox cycling as well as extended sonication were proven capable to temporally restore PL as well. Cyclic voltammetry of FMN onto SWNT forests indicated profound differences for the extended and collapsed FMN configurations in relation to oxygenated nanotube functionalities that act as mediators. These findings provide a fundamental understanding for flavin-related SWNT nanostructures that could ultimately find a number of usages in nanotube-mediated biosensing devices.