This study focused on studying the influence of the temperature and time on the functional diversity of the microbial populations involved in coffee (Coffea arabica) fermentation, using a shotgun metagenomic approach. Fermentations of depulped coffee grains were carried out under controlled and non-controlled temperature conditions for 24 h. Paired-end whole genome sequencing from mucilage samples was performed using an Illumina Hiseq 2x150 platform. Global and specific gene abundance was analyzed using the KEGG orthology (KO). Results showed a predominance of genes involved in carbohydrate and aminoacid metabolism during fermentations. The abundance of genes involved in glycolysis / gluconeogenesis, lactate fermentation and mixed acids were higher during fermentation conducted under non-controlled temperature conditions; however, fermentations carried out at 11 °C induced a significant increase in the abundance of genes involved in the synthesis of aminoacid, lipids and organic acids, as well as protein secretion systems. We concluded that different temperatures and conditions in fermentations produce appreciable changes on the functional potential of both aminoacid and carbohydrate metabolism, especially in the abundance of N- acetyl-lysine deacetylase, pyruvate dehydrogenase and 6-phosphofructokinase genes, which in turn could greatly affect the taste and quality of coffee. This information, together with the results from coffee cupping, provided valuable insights into the role microorganisms involved in coffee fermentation play in obtaining better taste attributes, as well to identify key genes and potential metabolic pathways associated with these special attributes.