Improving the nutritional quality of crops is crucial for human health, livestock, and agricultural productivity, especially on nutrient-limited soils. To address this, we investigated the variation and the genetic basis of mineral content, including, among others, calcium, iron, phosphorus, and zinc, in a diverse panel of maize (Zea mays L.) grown across environments. Our results show that genetic variation significantly contributes to differences in mineral content. Genotype-by-environment interaction and environmental factors, such as reduced phosphorus fertilisation, substantially impact the ionome composition, particularly decreasing zinc content and altering grain quality. Correlations between the 12 minerals were mostly positive, with variation observed in mineral composition between tissues and in translocation from vegetative to generative tissue. In addition, elite lines exhibited distinct mineral profiles compared to landraces. Genome-wide association mapping revealed a quantitative inheritance of the minerals and few common quantitative trait loci. Significantly associated markers were found in proximity to candidate genes involved in processes like mineral transport, detoxification and storage, which represent potential targets for marker-assisted selection to improve nutritional quality in maize. In conclusion, our results highlight the temporal and spatial dynamics of the maize ionome as a basis toward its targeted design for future agriculture. Summary statement: In maize (Zea mays L.), significant genetic variation exists for mineral content, with genotype-by-environment interactions influencing the ionome.Phosphorus fertilisation alters mineral profiles, and genome-wide association mapping revealed a quantitative inheritance and common QTL between minerals.