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Abstract Climate change adaptation requires building agricultural system resilience to warmer, drier climates. Increasing temporal plant diversity through crop rotation diversification increases yields of some crops under drought, but its potential to enhance crop drought resistance and the underlying mechanisms remain unclear. We conducted a drought manipulation experiment using rainout shelters embedded within a 36-year crop rotation diversity and no-till experiment in a temperate climate and measured a suite of soil and crop developmental and eco-physiological traits in the field and laboratory. We show that diversifying maize-soybean rotations with small grain cereals and cover crops mitigated maize water stress at the leaf and canopy scales and reduced yield losses to drought by 17.1 ± 6.1%, while no-till did not affect maize drought resistance. Path analysis showed a strong correlation between soil organic matter and lower maize water stress despite no significant differences in soil organic matter between rotations or tillage treatments. This positive relationship between soil organic matter and maize water status was not mediated by higher soil water retention or infiltration as often hypothesized, nor differential depth of root water uptake as measured with stable isotopes, suggesting that other mechanisms are at play. Crop rotation diversification is an underappreciated drought management tool to adapt crop production to climate change through managing for soil organic matter.