Superior soybean genotype selection for breeding programs involves several processes, which might be considered complex because important traits are mostly quantitative and highly influenced by the environment. This work was developed in order to evaluate the performance of recombinant soybean lines through genetic parameters and the performance of qualitative and quantitative agronomic traits, with emphasis on grain yield in low altitude regions. A total of 126 recombinant F10 soybean lines were evaluated in an augmented block design with three cultivars as interspersed checks. The traits assessed were: plant height (PH), number of pods per plant (NPP), first pod insertion height (FPIH), grain mass per plant (GMP), and grain yield (GY). Mixed models (REML/BLUP) were used to estimate the genetic parameters, and based on the BLUP predicted values, the multi-trait genotype–ideotype distance index (MGIDI) index was applied to select lines closest to the desired ideotype. High heritability values (>0.90) were observed for all characteristics assessed and experimental accuracy was also high. The MGIDI index selected the lines RIL18_IRC001, RIL103_IRC035, RIL73_IRC038, RIL124_IRC039, RIL71_IRC012, RIL115_IRC013, RIL113_IRC017, and RIL114_IRC038, which reached the greatest proximity to the intended agronomic ideotype. The line RIL13_IRC038 was selected simultaneously for reduction of FPIH and increase in PH, NPP, GMP, and GY, thus investment in this line is recommended. The use of mixed models and multi-trait indices maximizes the potential for selecting superior genotypes for future cultivars adapted to low-altitude environments.