Most molecular self-assembly strategies involve equilibrium systems, leading to a single thermodynamic product as a result of weak, reversible non-covalent interactions. Yet, strong non-covalent interactions may result in non-equilibrium self-assembly, in which structural diversity is achieved by forming several kinetic products based on a single covalent building block. We demonstrate that well-defined amphiphilic molecular systems based on perylene diimide/peptide conjugates exhibit kinetically controlled self-assembly in aqueous medium, enabling pathway-dependent assembly sequences, in which different organic nanostructures are evolved in a stepwise manner. The self-assembly process was characterized using UV/Vis circular dichroism (CD) spectroscopy, and cryogenic transmission electron microscopy (cryo-TEM). Our findings show that pathway-controlled self-assembly may significantly broaden the methodology of non-covalent synthesis.