The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (M) and the papain-like protease (PL) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe) which is an archetypal model of diselenides and a renowned potential therapeutic agent. The inhibitory concentration of (PhSe) against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via π-stacking and the mechanism of covalent (PhSe) + M product formation involving the catalytic residue C145, respectively. The CC (24.61 μM) and EC (2.39 μM) data indicate that (PhSe) is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The findings indicate potential mechanisms of proteases' inhibition by (PhSe); in particular, the results of the covalent inhibition here discussed for M, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.