This paper studies the abiotic properties and the microbial community of a pilot scale digester with a working volume capacity of 300 L. The system worked at mesophilic operating conditions, with several organic load rates formed by a mixture of different ratios between waste A (fruit and vegetable sludge + tomato waste) and waste B (pig slurry). The core group of microorganisms corresponding to the ratio 70% A:30% B, showed the highest methane production (60%). This core group included bacteria, principally Firmicutes and Bacteroidetes, involved in cellulolytic degradation, proteolysis and acidogenesis, as well as a concomitance between acetotrophic, mainly Methanosaeta methanogens and hydrogenotrophic, principally Methanosphaera and Methanobrevibacter methanogens. An increase of the proportion of waste B (pig slurry) to 50–60% resulted in a decrease of the production of biogas and methane, which unbalanced the methanogenic bacteria, increasing the amount of principally hydrogenotropic methanogens (Methanosphaera and Methanobrevibacter).