Antimicrobial peptides (AMPs) offer a great promise in designing new therapeutics due to their ability to interfere in bacterial growth by penetrating the cell wall. The overuse of antibiotics has resulted into antibiotic-resistant bacteria and AMPs could be an alternative to circumvent this resistance. Chitosan nanocrystals (ChsNCs) are rod-shaped polysaccharide-based nanomaterials, formed by deacetylation of seafood waste. They possess primary amino groups on the surface of the nanoparticles which can be as used a scaffold due to the built-in morphology and ease in functionalization. Here, we developed a new methodology to functionalize ChsNCs with amino acids and peptides by using fundamentals of solid phase peptide synthesis. The resulting functionalized rod-shaped nanomaterials were characterized using nuclear magnetic resonance (NMR), dynamic light scattering (DLS), zeta potential measurements and microscopy imaging. This synthetic strategy could be used in designing ChsNC-based nanomaterials to target specific cells by attaching bioactive peptides to the nanomaterial surface.