We calculate the amount of energy (kcal), macro- and micro-nutrients that were yearly produced from 1988 to 2017 in all of the 5563 Brazilian municipalities and disaggregated them according to the Food and Agriculture Organization of the United Nations's (FAO) information on whether the agricultural commodities were delivered to the food system as food, feed, seed, exported, processed, lost or used in other forms. We used nutritional information from 62 crops and 5 livestock categories to generate this dataset. Following De Ruiter, H., Macdiarmid, J. I., Matthews, R. B., & Smith, P. (2018 - doi:10.1016/j.gloenvcha.2018.06.007), we calculated the total production for 20 nutrients as well as their fractions delivered to the food system, described in the "read me" table. We organized the dataset in 20 TAB-delimited TEXT-files (.tab) of 22.3 Mb each.