Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing diversity in crops. This study was carried out at Lovely Professional University’s agricultural research farm in Punjab, India, during the year 2023. The experimental design followed a randomized complete block design (RCBD) with three replications. The experiment aimed to assess the effect of three chemical mutagens, sodium azide (SA), ethyl methyl sulphonates (EMSs), and methyl methane sulfonate (MMS), at three different concentrations (0.2%, 0.4%, and 0.6%), in SL958 and SL744 soybean varieties to select the mutant exhibiting the highest yield. The data were collected and analysed using a two-way ANOVA test through SPSS software (version 22), and the means were separated using Duncan’s multiple range test (DMRT) at the 5% level of significance. Between the two varieties, the highest seed germination percentage (76.0% seedlings/plot) was recorded in SL958 (0.4% SA), while the lowest (30.33% seedlings/plot) was observed in 0.6% MMS as compared to the control (53% and 76% in SL744 and SL958 at 10 days after sowing, respectively). Several weeks after sowing, the average plant height was observed to be higher (37.84 ± 1.32 cm) in SL958 (0.4% SA) and lower (20.58 ± 0.30 cm) in SL744 (0.6% SA), as compared to the controls (SL958: 26.09 ± 0.62 cm and SL744: 27.48 ± 0.74 cm). The average leaf count was the highest (234.33 ± 3.09 tetrafoliate leaves/plant) in SL958 (0.4% SA) while it was the lowest (87 leaves/plant) in 0.6% MMS as compared to the control (SL744 180.00 ± 1.63 and SL958 160.73 ± 1.05). The highest total leaf areas recorded in the SL958 and SL744 M1plants were 3625.8 ± 1.43 cm2 and 2311.03 ± 3.65 cm2, respectively. Seeds of the SL958 variety treated with 0.4% SA resulted in the development of tetrafoliate leaves with a broad leaf base and the maximum yield (277.55 ± 1.37 pods/plant) compared to the narrow pentafoliate leaves obtained through the treatment with EMS. Meanwhile, in the SL744 variety, the same treatment led to tetrafoliate leaves with a comparatively lower yield of 206.54 ± 23.47 pods/plant as compared to the control (SL744 164.33 ± 8.58 and SL958 229.86 ± 0.96). The highest protein content (47.04 ± 0.87% TSP) was recorded in the SL958 (0.4% SA) M2 seeds followed by a content of 46.14 ± 0.64% TSP in the SL744 (0.4% SA) M2 seeds, whereas the lowest content (38.13 ± 0.81% TSP) was found in SL958 (0.6% MMS). Similar observations were recorded for the lipid and fibre content. The 0.4% SA treatment in SL958 proved to be efficient in generating the highest leaf area (tetrafoliate leaves) and a reasonable yield of M1 (the first generation after mutation) plants.