Assessing the response of microbial communities to nutrient inputs in man-managed soils is of primary importance to understand the impact on ecosystem services provided by the soil microbiome. In this study, a low-nutrient soil was supplemented with seven different innovative fertilizers including matrixes of plant, animal, fungal or synthetic origin, and dosed to deliver the same amount of nitrogen. Growth of a potted grass crop (Cynodon dactylon) was recorded and the fertilizers were scored by the plant yield obtained in a greenhouse study. Soil was sampled at 9 and 58 days after the addition and bacterial community composition was analyzed after soil DNA extraction through pyrosequencing of 16S rDNA gene amplicons. Over 900 bacterial genera were detected, belonging to 21 described and 19 candidate phyla. In spite of the equal dose of nitrogen delivered, specific groups were fostered by given fertilizers; in particular marked effects on some phyla were displayed by a yeast-based fertilizer, which was also most effective in plant productivity. The main shifts were observed shortly after the fertilizer application, followed by a gradual stabilization of the equilibrium and by a rise in community evenness.