Inspired by spider silk's hierarchical diversity, we leveraged peptide motifs with the capability to tune structural arrangement for controlling the mechanical properties of a conventional polymer framework. The addition of nanofiller with hydrogen bonding sites was used as another pathway towards hierarchical tuning via matrix-filler interactions. Specifically, peptide-polyurea hybrids (PPUs) were combined with cellulose nanocrystals (CNCs) to develop mechanically-tunable nanocomposites via tailored matrix-filler interactions (or peptide-cellulose interactions). In this material platform, we explored the effect of these matrix-filler interactions on the secondary structure, hierarchical ordering, and mechanical properties of the peptide hybrid nanocomposites. Interactions between the peptide matrix and CNCs occur in all of the PPU/CNC nanocomposites, preventing α-helical ordering, but promoting inter-molecular hydrogen bonded β-sheet formation. Depending on peptide and CNC content, the Young's modulus varies from 10 to 150 MPa. Unlike conventional cellulose-reinforced polymer nanocomposites, the mechanical properties of these composite materials are dictated by a balance of CNC reinforcement, peptidic ordering, and microphase-separated morphology. This research highlights that leveraging peptide-cellulose interactions is a strategy to create materials with targeted mechanical properties for a specific application using a limited selection of building blocks.