Drought and insufficient nutrient supply are the main limiting factors for field crop production; therefore, the present study aimed to investigate the responses of four registered soybean varieties to limited nitrogen (N) supply in combination with drought stress. Plants were grown in tubes filled with silica sand, under open-air conditions. Water shortage was initiated at the three-leaf stage by providing 50% of water, and N deficiency was obtained by reducing the N content of the half-strength Hoagland solution by 50%. N deficiency did not influence the grain yield, while it significantly increased the root dry biomass in Boglár and Pannónia Kincse. Compared with nitrogen supply, the effects of the water shortage were dominant in root development. The expression levels of the investigated genes also showed genotypic variations. The expression of the Inducible nitrate reductase1 gene increased under N-deficient conditions in Boglár and decreased in Pannónia Kincse under drought conditions. The expression level of the aldehyde dehydrogenase gene and abscisic acid 8’-hydroxylase 3 increased under combined stress conditions. Summarising the agronomic and physiological characteristics, Boglár and Sinara were sensitive to drought, Bagera was sensitive to N deficiency but produced the highest yield under limited watering in each nitrogen treatment, while Pannónia Kincse was tolerant to nitrogen deficiency under well-watered conditions.