Biomaterials designed for tissue engineering applications should, among other requirements, mimic the native extracellular matrix (ECM) of the tissues to be regenerated, both in terms of biomimetic and mechanical properties. Ideally, the scaffold stiffness and stress resistance should be tuned for each specific implantation therapy. Self-assembling peptides (SAPs) are promising synthetic bionanomaterials prone to easy multi-functionalization, bestowing biomimetic properties. However, they usually yield soft and fragile hydrogels unsuited for the regeneration of medium-to-hard tissues. For this purpose, chemical cross-linking of SAPs is an option, but it often requires a moderately toxic and expensive chemical compound and/or the presence of specific residues/reactive sites, posing issues for its feasibility and translational potential. In this work, we introduced, characterized by rheology, atomic force microscopy (AFM), Thioflavin-T assay (ThT), and Fourier transform infrared (FT-IR) tests, and optimized (by tuning the power, temperature and treatment time) a novel fast, green and affordable methodology using mild microwave (MW) irradiation to increase the mechanical properties of diverse classes of SAPs. Low-power MWs increase stiffness, resilience, and β-structuration, while high-power MW treatments partially denature the tested SAPs. Our pure-physical methodology does not alter the SAP biomimetic properties (verified via in vitro tests of viability and differentiation of human neural stem cells), is compatible with already seeded cells, and is also synergic with genipin-based cross-linking of SAPs; therefore, it may become the next standard for SAP preparation in tissue engineering applications at hand of all research labs and in clinics.