Growth habit is one of the most important domestication traits in dry bean (Phaseolus vulgaris L.). In the U.S., Type II indeterminate upright varieties have helped farmers to switch from historic two-pass harvest to one-pass in direct harvest. Previous work suggested a stem diameter of 5.6 mm as threshold to select Type II architecture plants suitable for direct combining. In addition, the metabolic profile of indeterminate plants in dry bean is of great interest not only to define differences in seed coat color but to observe relationships with other traits, plant growth one of them. This study aimed to validate the correlation between stem diameter and other agronomic traits using breeding lines from a commercial program; further, this study investigates stem diameter as selection criteria to select genotypes that combine high seed yield and upright architecture, and to find genetic regions related to plant height, stem diameter and metabolic profile using a GWAS. Overall, mean stem diameter values were above 7.5 mm, higher than the proposed threshold of 5.6 mm. Stem diameter, showed no significant GxE interactions and the highest broad-sense heritabilities for pinto and slow darkening pinto. In market classes black, great northern, and navy plant height was the most relevant trait for seed yield variation, while stem diameter had low effect. In contrast, plant height and stem diameter are required to explain part of seed yield variability and continue selecting upright plants for pinto, red/pink, and SD-pinto. According to the GWAS, a region on chromosome Pv07 (40 Mb), was shared between plant height and stem diameter. Genes found in this region relate to plant growth and disease avoidance, which makes this region interesting to continue with further studies for plant architecture. Regarding metabolic studies GWAS identified a very interesting region on chromosome Pv01 (61.4 Mb), related to the enzyme Flavonoid 3'-monooxygenase / Flavonoid 3'-hydroxylase. This enzyme is present in the flavonoid biosynthesis pathway. However, it could also have relationship to plant growth. Further cloning of this region would be ideal to confirm differences in seed coat color and plant growth.