During fermentation, characteristics of sourdough-derived products are defined, not only from the fermentation substrate but also from the activity of the existing microbial community. Study of these functions can contribute to the identification of the specific metabolic processes that influence the products’ features, such as texture, taste or shelf life, in addition to the organisms performing them. On this basis, we evaluated, through metatranscriptome sequencing, the microbial gene expression activity levels and the processes taking place in 8 sourdough samples, collected from different locations in Greece. Results showed that the most active bacterial genera belonged to family Lactobacillaceae, while the most active yeast genera belonged to family Saccharomycetaceae. The majority of the most abundant identified KEGG functional orthologs (KEGGs) and Protein Families (Pfams) were involved in carbohydrate metabolism, while the remaining KEGGs and Pfams hits were related to fundamental cellular processes. Clusters of Orthologous Genes (COG) annotation revealed that the most abundant COG category was “G:Carbohydrate metabolism and transport” followed by category “J:Translation” and other processes related to fundamental cellular activities. Understanding all processes involved in sourdough fermentation enables us to control their activities and/or perform targeted interventions, in order to create new and improved sourdough products in terms of organoleptic characteristics, nutritional value, product quality and shelf life.