Nanoparticles (NPs) have left their mark on the field of bioengineering. Fabricated from metallic, magnetic, and metal oxide materials, their applications include drug delivery, bioimaging, and cell labeling. However, as they enter the body, the question remains - where do they go after fulfilling their designated function? As most materials used to produce NPs are not naturally found in the body, they are not biodegradable and may accumulate overtime. There is a lack of comprehensive, long-term studies assessing the biodistribution of non-biodegradable NPs for even the most widely studied NPs. There is a clear need for NPs produced from natural materials capable of degradation in vivo. As peptides exist naturally within the human body, their non-toxic and biocompatible nature comes as no surprise. Ultrashort peptides are aliphatic peptides designed with three to seven amino acids capable of self-assembling into helical fibers within macromolecular structures. Using a microfluidics flow-focusing approach, we produced different peptide-based NPs that were then three-dimensional (3D) printed with our novel printer setup. Herein, we describe the preparation method of NPs from ultrashort self-assembling peptides and their morphology in both manual and 3D-printed hydrogels, thus suggesting that peptide NPs are capable of withstanding the stresses involved in the printing process.