Urea is the final product of protein metabolism in mammals and can be found in different biological fluids. Use of mammalian urine in agricultural production as organic fertilizer requires safe handling to avoid the formation of ammonia that will decrease the fertilizer value due to the loss of nitrogen. Safe handling is also required to minimize the decomposition of urea into condensed products such as biuret and cyanuric acid, which will also have a negative impact on the potential sustainable production of crops and sanitation technologies. The study of thermodynamics and reaction kinetics of urea stabilization plays a key role in understanding the conditions under which undesirable compounds and impurities in urea-based fertilizers and urea-based selective catalytic reduction systems are formed. For this reason, we studied the reaction of urea in acid media to achieve urea stabilization by modeling the reaction of urea with sulfuric acid and phosphoric acid, and estimating the reaction enthalpy and adiabatic heat difference for control of the heat released from the neutralization step using Ca(OH)₂ or MgO for the safety of the process. Numerical and simulation analyses were performed by studying the effect of the surrounding temperature, the ratio of acid reagent to urea concentration, the rate of addition, and the reaction rate to estimate the required time to achieve an optimum value of urea conversion into ammonium dihydrogen phosphate or ammonium sulfate as potential technological opportunities for by-product valorization. Full conversion of urea was achieved in about 10 h for reaction rates in the order of 1 × 10⁻⁵s⁻¹ when the ratio of H₂SO₄ to CH₄N₂O was 1.5. When increasing the ratio to 10, the time required for full conversion was considerably reduced to 3 h.