Recurrent intermittent drought is a major constraint to cowpea productivity in sub-Saharan Africa, yet the physiological and phenological mechanisms underlying adaptation to sequential drought stress during flowering and podding stages remain poorly characterized. Twenty cowpea genotypes were evaluated under well-watered (WW) and recurrent intermittent drought stress (DS) conditions across two growing seasons to dissect genotype × environment (G × E) interactions and identify traits associated with drought adaptation. Drought stress was imposed as two sequential 10‑day cycles: the first during flowering, followed by rewatering, and the second during podding. A split-plot design was used, and data were analyzed using linear mixed-effects models, correlation analysis, additive main effects and multiplicative interaction (AMMI) analysis. Results revealed significant (
p
< 0.001 to
p
< 0.05) effects of genotype, water regime, and year effects for most traits, with complex interaction patterns, particularly for phenology and mid-season physiological responses. Grain yield was reduced from 1181.6 kg ha⁻
1
under WW to 1025.7 kg ha⁻
1
under DS, with substantial genotypic variation. The mean yield reduction across genotypes was 13.2%. Remarkably, IT17K-849–2-1 increased grain yield by 124 kg ha⁻
1
(+ 10.4%) under drought stress, representing the most notable positive drought response. The improved performance of IT17K-849–2-1 under drought was associated with higher chlorophyll retention and reduced canopy temperature. IT17K-1367–2-3 maintained the highest absolute yield under drought (1,492.5 kg ha⁻
1
) with a minimal penalty of − 50 kg ha⁻
1
(− 3.3%) while IT17K-1095–2-2 and UDS-CRs-F20-2 combined relatively high yield with greater stability across environments. Days to maturity (D95PM) showed a strong negative correlation with grain yield (r = -0.43*), confirming early maturity as a key drought escape mechanism. The Drought Tolerance Index ranged from 0.604 to 1.104, with a mean of 0.899. Overall, drought adaptation in cowpea is governed by the integration of phenological adjustment, physiological stability, and efficient water-use dynamics across developmental stages. IT17K-849–2-1, IT17K-1367–2-3, IT17K-1095–2-2, and UDS-CRs-F20-2 represent valuable genetic resources for breeding climate-resilient cowpea varieties.
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