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The development of aluminum (Al)‐tolerant cultivars is a complementary strategy to overcome the constraints caused by Al toxicity on acid soils and can contribute positively to the food supply for the growing global population. A major Al tolerance quantitative trait locus in maize is controlled by a citrate transporter encoded by ZmMATE1. Our goal was to evaluate the impact of the superior allele of ZmMATE1 on the yield performance of maize lines and hybrids cultivated on acid soils. Near‐isogenic lines carrying the superior allele of ZmMATE1, and the recurrent Al‐sensitive parent were crossed with elite lines, generating near‐isogenic hybrids contrasting for these alleles. All maize genotypes carrying this superior allele were more Al tolerant in nutrient solution than their isogenic counterparts having the ZmMATE1 allele derived from the Al‐sensitive parent. These genotypes were cultivated in control and Al stress soils for 2 yr. Aluminum toxicity caused a significant yield reduction of 18.7% for lines and 14.7% for hybrids over the 2 yr. The yield performance of maize genotypes declined in the second year compared with the first year, probably due to water deficiency after the grain‐filling stage. The superior allele of ZmMATE1 in maize hybrids conferred yield gains from 21 to 48% compared with the hybrids harboring the alternative allele in the Al stress soil in the first and second years, respectively. As this superior allele is rare in maize and is likely absent in several elite germplasms, molecular breeding based on ZmMATE1 can improve maize yield stability on acid soils. Core Ideas: High Al toxicity on acid soil causes a significant reduction in maize yield.The superior allele of ZmMATE1 improves maize yield on acid soil.Yield constraints on acid soil are ameliorated by this ZmMATE1 allele in maize hybrids.This ZmMATE1 allele is strategic in maize breeding to increase yield stability on acid soils. [ABSTRACT FROM AUTHOR]