The self-assembly of bolaamphiphile 1 into nanotubes containing a nanostructured electron donor/acceptor heterojunction is reported. In 10% MeOH/H2O, the tetraphenylporphyrin (TPP) and 1,4,5,8-naphthalenetetracarboxylic acid diimide chromophores engage in strong J-type pi-pi interactions within monolayer rings that further stack into the nanotube assemblies. In 10% MeOH/H2O at pH 1 or 11 or in pure MeOH, assembly is driven exclusively by the TPP ring, leading to the formation of nonspecific, unstructured aggregates. Steady-state, time-resolved fluorescence and femtosecond transient absorption spectroscopy revealed a strong dependence of the fluorescence decay and electron-transfer/charge-recombination time constants on the nature of the assemblies. These studies highlight the importance of local nanostructure in determining the photophysical properties of optoelectronic materials.