The interaction of nanoparticles (NPs) with proteins is widely investigated since it can be a key issue in addressing the problem of nanotoxicity, particularly in the case of biological and medical applications. In this work, silver and gold nanoparticles (AgNPs and AuNPs) were produced in water by Pulsed Laser Ablation in Liquid (PLAL) and allowed to react with Ubiquitin (Ub) (a small human protein essential for degradative processes in cells). NPs produced by PLAL are completely free of undesired contaminants and do not require the use of stabilizers. We found that the NPs+Ub system behaves differently if the NPs are or are not treated with a stabilizer before performing the interaction with Ub, since the presence of capping agents modifies the surface reactivity of the metal-NPs. The surface plasmon resonance (SPR) absorption spectroscopy was employed to monitor the fast changes occurring in the NP colloidal solutions upon interaction with Ub. The results obtained by SPR were confirmed by TEM analysis. Therefore, when Ub interacts with bare NPs a rapid aggregation occurs and, at the same time, Ub undergoes an amyloid transition. Notably, the aggregation of AuNPs occurs at a much greater rate than that of analogous AgNPs and the Ub fibrils that are formed can be imaged by thioflavin T fluorescence.