Brazil holds a series of favorable climatic conditions for agricultural production including the hours and intensity of sunlight, the availability of agricultural land and water resources, as well as diverse climates, soils and biomes. Amidst such diversity, Brazilian coffee producers have obtained various standards of qualities and aromas, between the arabica and robusta species, which each present a wide variety of lineages. However, temperatures in coffee producing municipalities in Brazil have increased by about 0.25 °C per decade and annual precipitation has decreased. Therefore, the agricultural sector may face serious challenges in the upcoming decades due to crop sensitivity to water shortages and thermal stress. Furthermore, higher temperatures may reduce the quality of the culture and increase pressure from pests and diseases, reducing worldwide agricultural production. The impacts of climate change directly affect the coffee microbiota. Within the climate change scenario, aflatoxins, which are more toxic than OTA, may become dominant, promoting greater food insecurity surrounding coffee production. Thus, closer attention on the part of authorities is fundamental to stimulate replacement of areas that are apt for coffee production, in line with changes in climate zoning, in order to avoid scarcity of coffee in the world market.