The modulation of the hierarchical nucleated self-assembly of tri-β3-peptides has been studied. β3-Tyrosine provided a handle to control the assembly process through host-guest interactions with CB and CB. By varying the cavity size from CB to CB distinct phases of assembling tri-β3-peptides were arrested. Given the limited size of the CB cavity, only one aromatic β3-tyrosine can be simultaneously hosted and, hence, CB was primarily acting as an inhibitor of self-assembly. In strong contrast, the larger CB can form a ternary complex with two aromatic amino acids and hence CB was acting primarily as cross-linker of multiple fibers and promoting the formation of larger aggregates. General insights on modulating supramolecular assembly can lead to new ways to introduce functionality in supramolecular polymers.