We incorporate various gold nanoparticles (AuNPs) capped with different ligands in two-dimensional films and three-dimensional aggregates derived from N-stearoyl-L-alanine and N-lauroyl-L-alanine, respectively. The assemblies of N-stearoyl-L-alanine afforded stable films at the air–water interface. More compact assemblies were formed upon incorporation of AuNPs in the air–water interface of N-stearoyl-L-alanine. We then examined the effects of incorporation of various AuNPs functionalized with different capping ligands in three-dimensional assemblies of N-lauroyl-L-alanine, a compound that formed a gel in hydrocarbons. The profound influence of nanoparticle incorporation into physical gels was evident from evaluation of various microscopic and bulk properties. The interaction of AuNPs with the gelator assembly was found to depend critically on the capping ligands protecting the Au surface of the gold nanoparticles. Transmission electron microscopy (TEM) showed a long-range directional assembly of certain AuNPs along the gel fibers. Scanning electron microscopy (SEM) images of the freeze-dried gels and nanocomposites indicate that the morphological transformation in the composite microstructures depends significantly on the capping agent of the nanoparticles. Differential scanning calorimetry (DSC) showed that gel formation from sol occurred at a lower temperature upon incorporation of AuNPs having capping ligands that were able to align and noncovalently interact with the gel fibers. Rheological studies indicate that the gel–nanoparticle composites exhibit significantly greater viscoelasticity compared to the native gel alone when the capping ligands are able to interact through interdigitation into the gelator assembly. Thus, it was possible to define a clear relationship between the materials and the molecular-level properties by means of manipulation of the information inscribed on the NP surface.