Potassium (K) improves the stress tolerance of crop plants, which varies on the timing of K application and crop varieties. Soybean is a promising crop that can easily fit with the cropping pattern during kharif I season, when water logging occurs due to sudden rain. Therefore, an experiment was conducted to determine the effect of K management on the productivity and seed quality of soybean under normal and waterlogged conditions. The treatments comprised three factors, namely soybean genotypes (BU Soybean-1 and BU Soybean-2), waterlogging (WL) (control and WL for 4 days at the flowering stage (FS)), and K application (full dose as basal and 50% as basal +50% as top dress after termination of the flooding). The trial was laid out in a randomized complete block design with three replications. Findings revealed that BU Soybean-1 produced a higher number of pods and seeds pod−1 under control conditions with basal application of K. On the other hand, BU Soybean-2 produced taller plants and heavier grain, improving grain and straw yield under WL conditions when K was top dressed. The varieties absorbed a higher amount of nitrogen, phosphorus, and potassium under control conditions compared to WL when K was top dressed. Similarly, the seed protein content of both varieties was higher in the control condition with a top dressing of K. However, a higher percentage of seed germination was obtained from BU Soybean-2 in the control condition with a top dressing of K. Further, more electrical conductivity and more mean germination time were recorded in the case of BU Soybean-2 under WL with the basal application of K. Split application of 50% of recommended K fertilizer after the recession of flood water could be suggested for improved grain yield in flood-affected soybean growing areas.