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To construct this database, we integrate the nutritional content of 62 crops and 5 livestock categories to estimate the amount of 21 macro and micro-nutrients (including energy) that were produced from agriculture in each Brazilian municipality during the last three decades. Additionally, we allocate these nutrients according to their share in the food system (for example, human food, animal feed, export etc.). It is a unique data source on macro and micro-nutrients availability for human consumption and animal feed, but also regarding another aspects of the food system, such as international agricultural trade, energy production (for example, in the form of ethanol) or post-harvest and post-processing losses, from local to national levels, in a wide time frame of 30 years. This database can be used in scientific research regarding food and nutrition security and in the construction of indicators for monitoring food and agricultural programs and policies that aim at the promotion of food and nutritional security. Also, it has the potential to enable broader analysis of the food system as whole in terms of food stability and resilience.