Soybean is one of the important crops and is much needed by people in Indonesia. Most soybean needs in Indonesia are still imported because domestic production is still low. The low soybean production in Indonesia is partly due to the lack of availability of superior varieties that are able to adapt to the environment and the application of cultivation technology that has not been optimal by farmers. The aim of this research is to obtain the best dose and the mutant line of Kipas Merah and the best combination of both in a sub-optimal environment. This study used a factorial randomized block design 3 x 7 with 3 replications. The dose of NPK fertilizer is the first factor consisting of 3 levels (200 kg ha−1, 300 kg ha−1, and 400 kg ha−1). While the second factor is a mutant line of Kipas Merah (A1, A2, A7, A11, and A14), and in addition, as the comparison, we used Kipas Merah (parent) and Deja2 variety. The results showed that the treatment dose of Phonska NPK fertilizer (15:15:15) was better found in the application of a fertilizer dose of 400 kg ha−1 on the parameters a number of seeds per plant, the weight of seeds per plant, the weight of 100 seeds, the weight of seeds per plot and potential yield. The best mutant lines among the tested lines were the A1 and A11 mutant lines. The best A1 line was on the number of seeds per plant and weight of seeds per plant, while A11 was best on parameters of seed weight per plant, the weight of 100 seeds, the weight of seeds per plot, and yield potential.