The construction of an n–p heterojunction through the self-assembly of a dyad based on tetraphenylporphyrin (TPP) and 1,4,5,8-naphthalenedimide (NDI) (1) is described. Proton transfer from the lysine head group of 1 to the porphyrin ring occurs concomitantly with self-assembly into 1D nanorods in CHCl3. TEM and AFM studies showed that the nanorods are formed by the lateral and vertical fusion of multilameller vesicles into networks and hollow ribbons, respectively. These intermediate structures transitioned to nanorods over the course of 4–6 days. Time-resolved spectroscopy revealed that photoinduced charge separation occurs with rate constants that depend on the nature of the aggregation.