The aim of the present study was to assess the influence of innovative plant-based fertilisers on soil microbial functional diversity in organically managed soil. Five fertilisers were chosen for the comparison: fresh red clover biomass (RC), fermented red clover biomass (FerRC), fermented pea and spring wheat biomass (FerP+W), composted red clover and straw biomass (ComRC+S), granulated cattle manure (GCM). Measurements of microbial functional diversity were recorded at two weeks, four months and 14 months after fertilisation. The findings of this study suggested that functional diversity of microbial communities was greater in soil fertilised with organic plant-based fertilisers than with no fertiliser treatment. Averaging across the utilisation of all 31 carbon sources, differences in average well colour developing (AWCD) across fertilised soils were not significant; however, there were significant differences in AWCD between the six different carbon substrate groups. The study also demonstrates important impacts of time: two weeks after fertlisers incorporation, microbial metabolic potential increases in complex carbon and amines substrates in RC, FerRC and GCM; four months later, the significantly greater utilisation is estimated for carbohydrates in GCM and ComRC+S; and the highest utilisation ratio was reached after 14 months in the amino acid substrates group in RC and GCM.