This study aimed to evaluate the response of four soybean cultivars (Arisoy, Cinsoy, Umut-2002, and Sarigelin-1) in terms of their mineral and morpho-physiological properties to waterlogging stress during the early growing stage (V1). 20-day-old plants were exposed to waterlogging for 14 days. The results showed that soybean cultivars reacted differently to waterlogging. The shoot and root fresh weight and chlorophyll rate were significantly lower in the waterlogged plants than in the control. No significant changes in shoot and root fresh weights of cv. Cinsoy was observed due to waterlogging while cv. Cinsoy had the highest chlorophyll rate. Waterlogging led to decreasing the phosphorus concentration, but Ca, Na, Zn, Mn, B, and Cu were enhanced. However, cv. Arisoy possessed higher K, P, Ca, Mg, S, and B levels than the control, and a significant reduction in Ca, S, Zn, Mn, B, Cu, and K/Na ratio was determined in the waterlogged plants. Phosphorus was decreased in all the cultivars except for cv. Arisoy. It was concluded that Arisoy and Cinsoy appeared more tolerant to waterlogging during the early growing stage compared to the other soybean cultivars, and the stress mainly affected the plant's mineral concentrations.