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Different nitrogen (N) sources have been reported to significantly affect the activities and expressions of N metabolism enzymes and mineral elements concentrations in crop plants. However, molybdenum-induced effects in winter wheat cultivars have still not been investigated under different N sources. Here, a hydroponic study was carried out to investigate these effects on two winter wheat cultivars (‘97003’ and ‘97014’) as Mo-efficient and Mo-inefficient, respectively, under different N sources (NO₃^−, NH₄NO₃, and NH₄⁺). The results revealed that the activities of nitrate reductase (NR) and nitrite reductase (NiR) followed the order of NH₄NO₃ > NO₃^− > NH₄⁺ sources, while glutamine synthetase (GS) and glutamate synthase (GOGAT) followed the order of NH₄⁺ > NH₄NO₃ > NO₃^− in both the wheat cultivars. However, Mo-induced effects in the activities and expressions of N metabolism enzymes under different N sources followed the order of NH₄NO₃ > NO₃^− > NH₄⁺ sources, indicating that Mo has more complementary effects towards nitrate nutrition than the sole ammonium source in winter wheat. Interestingly, under −Mo-deprived conditions, cultivar ‘97003’ recorded more pronounced alterations in Mo-dependent parameters than ‘97014’ cultivar. Moreover, Mo application increased the proteins, amino acids, ammonium, and nitrite contents while concomitantly decreasing the nitrate contents in the same order of NH₄NO₃ > NO₃^− > NH₄⁺ sources that coincides with the Mo-induced N enzymes activities and expressions. The findings of the present study indicated that Mo plays a key role in regulating the N metabolism enzymes and assimilatory products under all the three N sources; however, the extent of complementation exists in the order of NH₄NO₃ > NO₃^− > NH₄⁺ sources in winter wheat. In addition, it was revealed that mineral elements profiles were mainly affected by different N sources, while Mo application generally had no significant effects on the mineral elements contents in the winter wheat leaves under different N sources.