The aim of this study was to determine the impact of using mineral fertilizers on biogas production from vegetable waste. A mixture of wastes from a fruit and vegetable processing plant was used in the experiments, together with two commercial fertilizers, Substral and Agrecol. Experiments were conducted in 5-L anaerobic reactors operated semi-continuously at 35 °C. The application of Substral at a dose of 1 g/kg increased the production of methane and hydrogen by 40% and 78%, up to 420 LCH4/kgVS and 34 LH2/kgVS, respectively. In contrast, with Agrecol supplementation, the average yields of methane and hydrogen were 365 LCH4/kgVS and 27.7 LH2/kgVS, respectively. The beneficial effects of supplementation were due to the compositions of the mineral fertilizers, which contained nutrients and metals that stimulate the growth of microorganisms and build the structures of enzymes. The addition of mineral fertilizers changed the microbial communities of the digestates. At a family level, the main bacteria groups reported were Lactobacillaceae, Anaerolineaceae, Clostridiaceae, Synergistaceae, and Bacteroidetes vadin HA17. The predominant methanogens were Methanosarcinaceae and Methanosaetaceae. There was no clear relationship between the supplementation type and dose and the growth of individual microbial groups. However, the addition of mineral fertilizers increased the relative abundance of Lactobacillaceae and Anaerolineaceae, which are responsible for the hydrolysis and fermentation of polysaccharides into lactic acid, hydrogen, and acetic acid.