Due to inadequate efforts to reinforce nitrogen fixation capability of bean via symbiosis with rhizobia, improvement of bean productivity is still highly dependent on chemical fertilization. An advanced understanding of agro-ecosystem-bean-Rhizobium interaction is required to improve symbiosis efficiency. Thus, seasonal development of rhizobial nodulation was characterized according to 20 agro-ecological properties for 122 commercial bean fields. Principal component analysis identified soil texture as a major descriptor of agrosystem-bean-disease-Rhizobium interaction. Nonparametric correlation analysis indicated significant associations of root nodulation with bean class, fungicidal treatment of seed and soil, Fusarium root rot index, planting date and depth, soil texture, clay and sand content. Ordinal regression analysis demonstrated that rhizobial nodulation was improved by applying initial drought, heavier soil textures with greater organic matter and neutral pH, using herbicides and manure, growing white beans, irrigating every 7–9 days, later sowing in June, reducing disease and weed, shallower seeding, sowing beans after alfalfa, avoiding fungicidal treatment of seed and soil, and omitting urea application. This largescale study provided novel information on a comprehensive number of agronomic practices as potential tools for improving bean-Rhizobium symbiosis for sustainable legume production systems.