Nejayote, the wastewater from the nixtamalization of maize, is difficult to biodegrade due to its abundant calcium content; low levels of nitrogen, phosphorus, and easily assimilable sugars; elevated pH; and high chemical oxygen demand (COD). The aim of the present study was to isolate microorganisms capable of utilizing filtered nejayote (NEM) as the only source of carbon for growth and to test the best microorganism for the bioremediation of this wastewater by lowering the level of pH and COD. Of the 15 strains of microorganisms tested, Rhodotorula mucilaginosa LCRE was chosen and identified using molecular techniques. Subsequently, its growth kinetics were characterized during cultivation in unenriched NEM (control) and NEM enriched with nitrogen and phosphorus salts. R. mucilaginosa LCRE showed a greater growth (6.9 ≤ X ≤ 8.9 g L−1), biomass yield (0.33 ≤ YX/S ≤ 0.39 g g−1), and specific growth rate (0.748 ≤ µ ≤ 0.80 day−1) in the enriched versus control NEM (X = 6.55 g L−1, YX/S = 0.28 g g−1, and µ = 0.59 day−1). However, a higher total sugar consumption (94.98%), better COD removal efficiency (75.5%), and greater overall COD removal rate (1.73 g L−1 h−1) were found in the control NEM. Hence, R. mucilaginosa LCRE holds promise for the efficient bioremediation of nejayote without costly pretreatments or nutrient supplementation.