Neonicotinoid seed treatments protect maize during early growth but can induce phytotoxicity that intensifies during storage. Despite recognized genotypic variation in tolerance, standardized phenotyping methods are lacking. We evaluated nine commercial maize hybrids under three seed treatments (control, one neonicotinoid [1N], and two neonicotinoids [2N]) across two storage periods (0 and 6 months at 25 °C) using germination, accelerated aging, and cold tests. A Seed Treatment Tolerance Index (STTI) was analyzed through hierarchical clustering, principal component analysis, and multivariate analysis of variance. Results showed a significant triple interaction among genotype, seed treatment, and storage. Hybrids from female line A maintained STTI above 0.95, while female C hybrids showed germination reductions up to 48 percentage points and vigor losses up to 90 percentage points under 2N after six months. Tolerance was associated with hydrogen peroxide regulation by catalase and ascorbate peroxidase. The STTI proved a reliable tool for classifying genotypic tolerance, with direct applications for breeding programs and seed industry logistics.