This dataset contains the data related to the set of experiments of BIOCTANE WP1- Module 1 - Task 1.3 - Two-stage fermentation strategy for selective propionate production with mixed cultures. The aim of this experiment was to the investigate a two-stage fermentation strategy to first convert food waste to lactate, and then to propionate and acetate, with adjusted operating conditions (pH and temperature). Two mixed inocula were used: activated sludge and compost leachate in order to compare their performance regarding lactate production and subsequent propionate production from lactate. The data contain information on the operating conditions, the metabolic profiles obtained at the beginning and the end of each stage, and the microbial communities composition for each stage. README.MB.txt file provides a detailed description of the data. These data underpinned a journal article and an oral presentation for a conference.