Grain yield in Zea mays (maize), as in all crops, is an integration of germplasm and environment across the growing season. To improve an integrative phenotype such as grain yield is challenging when molecular and physiological traits that drive the grain yield interact with the multitude of potential environmental conditions in which they are expressed. To examine this interaction, 31 phenotypic traits (including yield), 83 annotated metabolites, and nearly 22,000 transcripts were assessed from a set of 57 diverse maize hybrids grown in three environments across the central USA corn-belt. Despite a significant level of variability in measured characteristics, phenotypic traits and gene expression levels were found to be more consistent across environments and formed a complex picture of interacting variables impacting grain yield. Whole-plant phenotypic traits, developmental phenology, plant height and kernel row number largely controlled by genetics effects. Grain yield and associated yield components, biomass, root growth and nitrogen traits, however, were principally controlled by environment. Phenology traits and nitrogen content showed the most consistent correlation with yield across environments in the tested commercial hybrids. Continued improvement of maize grain yields requires an understanding of baseline variation of genes and plant phenotypic traits that are penetrant across commercially-relevant germplasm.