Microbial inoculants are increasingly proposed within ecological-intensification strategies, yet their performance under heterogeneous commercial conditions remains uncertain. We evaluated a tripartite consortium of Funneliformis mosseae, Naganishia albida, and Bacillus tequilensis across six tomato production sites in central Chile using a 2 × 2 factorial randomized complete block design (irrigation × microbial management; three blocks per site; 72 plots). Normal irrigation was compared with reduced irrigation designed to receive 38% of the nominal irrigation depth. The same plots were followed across two growing seasons differing in fertilization and crop-management practices. Soil properties, arbuscular mycorrhizal (AM) colonization, enzyme activities, substrate-induced responses, plant physiology, biomass, and yield were assessed. Site and growing-season context strongly structured responses. Consortium application increased total AM colonization from 46.18% to 52.47% (p < 0.001; partial η² = 0.176) and altered substrate-use composition (p = 0.009). The simple-sugars-to-other-substrates ILR balance increased under consortium application (Holm-adjusted p = 0.005), while the glucose-to-fructose balance decreased (Holm-adjusted p = 0.004), without increasing overall respiratory activity. Total and commercial yield showed no significant consortium response, and reduced irrigation did not enhance agronomic responses. Field evaluation of microbial inoculants should therefore prioritize agronomic outcomes across production contexts rather than colonization alone.