The amphiphilic self-assembling peptide EAK16-II was found to be able to stabilize hydrophobic compounds in aqueous solution. Micro/nanocrystals of a hydrophobic compound, pyrene, and a hydrophobic anticancer agent, ellipticine, were stabilized by EAK16-II to form colloidal suspensions in water. Initial evidence of the association between EAK16-II and hydrophobic compounds was the observation of a clouding phenomenon and a difference in fluorescence spectra of the solution. A further investigation on the interaction between EAK16-II and pyrene was carried out using fluorescence spectroscopy and scanning electron microscopy (SEM). It was found that the pyrene–peptide complex formation required mechanical stirring, and the freshly prepared peptide solution (containing peptide monomers and/or peptide protofibrils) was more effective at stabilizing pyrene than the mature fibrils in aged peptide solutions. The time duration over which the complex formed was about 22h. The data on the complexation of pyrene and EAK16-II at various concentrations suggested that the maximum amount of stabilized pyrene was concentration dependent. SEM images showed that peptide concentration did not significantly affect the size of the complexes/suspensions but altered the structures of the peptide coating on the surface of the complex. Atomic force microscopy (AFM) was conducted to study the interaction of EAK16-II with a model hydrophobic surface, which provided some detailed information of how peptide adsorbed onto the hydrophobic compounds and stabilize them. This study shows the potential of self-assembling peptides for encapsulation of hydrophobic compounds.