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Abstract The application of biochar and gypsum to soil promotes soil health for crop production. The benefits can vary depending on the soil and climate. We evaluated seed yield, quality, and soil quality benefits of applying biochar and gypsum to silt loam soil in a humid subtropical climate at Stoneville, MS (33° 42′ N, 90° 55′ W). Sugarcane ( Saccharum officinarum L.) bagasse‐based biochar was applied at 10 (B1) and 25 Mg ha −1 (B2). Gypsum, a flue gas desulfurization product, was applied at 2.24 (G1) and 6.72 Mg ha −1 (G2) from 2020 to 2022, and data were collected up to 2024 and compared against a control treatment with no soil amendments (CC). In the 5 years, soybean seed yields were highest under G1. When the rainfall received was substantially low, in 2022 and 2024, CC resulted in the lowest yield, showing gypsum and biochar amendments’ positive impact on soil conditions for soybean growth under drought. Under severe drought, in 2024, all four treatments resulted in significantly higher yields, from 17% under B1 to 38% under G1, than CC, indicating substantial benefits from using biochar and gypsum as soil amendments in rainfed soybean production in the region without affecting quality. The study also revealed the efficacy of gypsum in transforming soil chemistry, positively impacting soybean yield. G1 was more effective as a soil amendment for stabilizing rainfed soybean productivity. Repeating the study across soils and climates in the region can help develop robust recommendations for using soil amendments for sustainable rainfed crop production.