Urease is a key metalloenzyme with broad industrial, agricultural, and medical relevance, and it is implicated in the virulence of numerous pathogenic microorganisms. Elevated urease activity supports the persistence of urease-producing microbes and contributes to nitrogen depletion in agricultural soils. Inhibitors of urease that are effective are therefore discovered and their discovery would be a plus. This research is looking at the possibility of amino acids being the safe, biocompatible, and effective urease inhibitors with prospective use in agriculture and medicine. The inhibition potentials of L-Valine, D-Phenylalanine, L-Methionine, L-Tyrosine, L-Arginine, and D-Threonine (Val, Phe, Met, Tyr, Arg, and Thr for short) against jack bean urease were evaluated systematically. The varying side-chain chemistries (aromatic, sulfur, hydroxyl, and ionic) of these compounds that could be involved in urease binding were the basis for selection. The study showed that Phe (IC50 = 0.53 μM) and Val (0.57 μM) were the strongest inhibitors, followed by Met (0.97 μM) and Arg (1.15 μM). A moderate level of inhibition was noted for Tyr (2.38 μM) and Thr (3.97 μM) was singled out as the least effective inhibitor. In vitro results have been validated by molecular docking and MM-GBSA calculations, which are in excellent agreement, as ligands with the highest predicted binding energies are also those with the lowest IC50 values. The conclusion reached is that natural amino acids can be considered non-toxic and environmentally friendly urease inhibitors for both agricultural soil management and the treatment of urease-associated infections.