The combined effect of temperature-adapted inocula and anaerobic fermentation (AF) settings (pH 5.1 and 50 ◦C) were assessed to produce short-chain carboxylates (SCCs). In this study, the AF of carrot pulp was investigated using inocula adapted at different temperatures (25, 35, and 55 ◦C) with the aim of shifting the microbiome activity from biogas to SCC production. The highest SCC content (17.2 g COD L−1), and bioconversion (26.1%) and acidification efficiency (56.3%) were achieved with 35 ◦C-adapted inoculum. Lactic acid production prevailed in all reactors, demonstrating a high selectivity in SCC production. Both the microbial richness and diversity sharply diminished in the 35 ◦C and 55 ◦C operated reactors, with Firmicutes phylum identified as key players of the lactic acid production in AF. The results demonstrated that the operating temperature played a key role in shaping the microbial structure of inocula, leading to different process performances and highlighting thermophilic AF as a feasible process to produce lactic acid.