Maize (Zea mays L.) is native to Mexico, in which wide genetic diversity can be found; however, maize is at risk of genetic erosion, and agroforestry systems (ASs) can be a strategy for conservation and sustainable use of this crop. The objective of this study was to evaluate the variation in the morpho-agronomic characteristics of three native maize races, Tuxpeño, Olotillo × Tuxpeño and Ratón × Tepecintle, cultivated in different AS in a tropical climate of Veracruz, Mexico, as well as its association with microclimatic conditions. In 2019, experiments were established in the localities La Gloria and La Luisa, Veracruz, where the three maize races are cultivated, in a randomized complete block design with three replications in a 3 × 4 factorial scheme (three native maize races and three AS arrrays, plus monoculture). Ten morpho-agronomic variables were recorded in each experiment and were analyzed by analysis of variance (ANOVA; Tukey’s post-hoc test, all p ≤ 0.05) and principal component analysis (PCA). Six morpho-agronomic characteristics showed significant differences for the race × system interaction. Consistently standing out both in the Myroxylon with 2.8 m × 2.0 arrays and in the monoculture was the Olotillo × Tuxpeño race, as there were no variations (p ≥ 0.05) in 50% of its morpho-agronomic characteristics. The first three PCs explained 87.7% of the cumulative variance, determined by five variables of the ears, three of the grain and plant height, which were associated with temperature; therefore, the microclimatic conditions of the studied ASs are associated with the morpho-agronomic characteristics of the native maize races. The results show that ASs could be a strategy for the conservation and use of native corn germplasm and could allow the diversification of sustainable production for rural farmers.