This dataset includes nutritional and agronomic traits collected from a multi-parent advanced generation intercross (MAGIC) population of cowpea grown in California during 2016–2017. The data were used in QTL mapping and genomic prediction as part of the manuscript entitled "Quantitative trait loci and genomic prediction for grain sugar and mineral  concentrations of cowpea [Vigna unguiculata (L.) Walp.]"

Grain sugar concentrations were assayed using high-performance liquid chromatography. Grain mineral concentrations were determined by inductively coupled plasma–optical emission spectrometry and combustion.

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