Improvement of agronomic and seed quality traits in soybean [Glycine max (L.) Merr.] occurs in breeding programs as a result of crossing elite soybean genotypes and selection of superior offspring in each cycle. The objective of this study was to evaluate changes in traits over 100 yr of selection in Ontario, Canada, in two soybean breeding programs at the University of Guelph: Guelph Campus (Maturity Group [MG] 0 and I) and Ridgetown Campus (MG II) programs. Fifty‐six Guelph cultivars (released between 1983 and 2016), 46 Ridgetown cultivars (released between 1987 and 2015), and 37 Guelph‐pedigree related historical cultivars (from 1913 to 1985) were grown in field trials over 3 yr (Guelph Campus) and 2 yr (Ridgetown Campus) at two locations per breeding program to measure 13 traits. Yield increased in the Guelph Campus cultivars by 17.1 kg ha−1 yr−1 and by 15.7 kg ha−1 yr−1 in the Ridgetown Campus cultivars, while yield per day of maturity per year of release significantly increased in elite cultivars. Protein in the Ridgetown Campus cultivars increased at 0.76 g kg−1 yr−1, whereas the Guelph Campus cultivars showed no trend. In Ridgetown Campus cultivars 100‐seed weight significantly increased at 0.1 g yr−1. Within the historical cultivars, 100‐seed weight was significantly correlated with both protein (r = 0.50) and oil (r = −0.42). Genotype × trait biplot analyses revealed differential patterns of trait relationships between the elite and historical cultivars. Oil and yield were associated within the Guelph Campus cultivars. The association of 100‐seed weight and protein was only found in the historical cultivars. Yield has increased in both breeding programs while seed traits have been altered over time.