Advances in nanotechnology have indicated that the passivant and the inorganic surface play a pivotal role in controlling the structure/function relationship of materials. Beyond standard materials-based methods, bioligands have recently demonstrated the production of unique nanomaterial morphologies for application under ambient conditions for multiple activities, such as catalysis and biosensing. We have recently demonstrated that a biotemplate technique could be employed to produce spherical and linear Pd nanostructures in water using a self-assembling peptide framework. The materials possessed high catalytic reactivity that was controlled by the three-dimensional structure of the composite materials. To investigate the effect of the peptide template on the reactivity of Pd nanostructures, an in depth analysis of the catalytic activity of Pd nanostructures fabricated via truncated templates is presented. The new templates were designed from portions of the original framework, which demonstrated unique synthetic and functionality control. Two different reactions, Stille C-C coupling and 4-nitrophenol reduction, were employed to ascertain the effect of template structure on the reactivity of synthesized Pd nanomaterials via changes in reagent diffusion through the bioscaffold. The results indicate that the peptide framework plays an important role and could be used to tune and optimize the functionality of the final composite materials for the target application.