Peptide-based molecules and their hydrogels are useful materials for biomedical applications due to the reversible nature of their self-assembly as well as the diversity of nanostructures that can be created starting from low-molecular weight compounds. In this study, we have focused on comprehending the characteristics of fibrillar networks of l-lysine-based self-assembled dipeptide hydrogels with a focus on their antibacterial properties. For that purpose, l-lysine has been complemented with hydrophobic aromatic moieties coming from l-phenylalanine and benzyloxyxarbonyl N-capping. In addition, the peptide C-terminus is blocked with alkylamides of different chain lengths which introduces additional dispersive interactions and hydrophobicity. These materials were well characterized by transmission electron microscopy, scanning electron microscopy, wide-angle powder X-ray diffraction and oscillatory rheology. Finally, biocompatibility and antimicrobial tests were performed showing that these hydrogels are compatible with HEK 293 cells and present a remarkable antibacterial activity against both Gram positive (S. aureus) and Gram negative (E. coli) bacteria.