Further understanding of the interactions between nanoparticles (NPs) and biological molecules offers new possibilities in the applications of nanomedicine and nanodiagnostics. The properties of NPs, including size, shape, and surface functionality, play a decisive role in these interactions. Herein, we evaluated the influences of gold NPs (AuNPs) with different sizes (5-60 nm) and shapes (i.e., spherical, rod, and cage) on the self assembly of diphenylalanine (Phe-Phe) dipeptides. We found that the size of AuNPs smaller than 10 nm did not affect the self-assembly process of Phe-Phe, while bigger AuNPs (>10 nm) caused the formation of starlike peptide morphologies connected to one center. In the case of shape differences, nanorod and nanocage morphologies acted differently than spherical ones and caused the formation of densely packed, networklike dipeptide morphologies. In addition to these experiments, by combining photothermal properties of AuNPs with a Phe-Phe-based organogel having a thermo-responsive property, we demonstrated that the degelation process of AuNPs embedded organogels may be controlled by laser illumination. Complete degelation was achieved in about 10 min. We believe that such control may open the door to new opportunities for a number of applications, such as controlled release of drugs and tissue engineering.