Objectives The primary metabolite contents of ripe fruits result from complex regulations during their development. For Solanaceae, these regulations have been widely studied in tomato. The fruit metabolite contents of other fruit species, such as pepper (Capsicum annuum L.) and eggplant (Solanum melongena L.), constitute a valuable resource for the community to study the regulation of fruit metabolism and identify common or species-dependent regulations. This dataset about major polar metabolites is part of a larger project that integrates other omics data for pepper and eggplant, and other fruit species for metabolomics and other omics. Data description We provide quantitative metabolite data of pepper and eggplant fruit along development. We sampled pepper and eggplant fruit cultivated in a tunnel or a greenhouse at 10 or 11 stages from anthesis to ripe fruit. We used proton nuclear magnetic resonance (1H-NMR) metabolomic profling of polar extracts to quantify the major metabolites and expressed the data in µmol per g fresh weight. Twenty-four metabolites were determined in pepper and 27 in eggplant. Nineteen common metabolites were quantifed in both fruit species including three soluble sugars and one sugar-alcohol, fve organic acids and nine free amino acids. These data can be combined with similar quantitative data on other species or complemented with other omics data to perform cross-species or cross-omics comparisons.