In a sustainable agriculture farming systems experiment, soils managed under organic farming practices had greater microbial abundance and activity, and higher numbers of bacterial-feeding nematodes during crop growth, than those managed under conventional fanning practices. We tested rates of organic matter decomposition in the two soils and monitored the abundance and activity of soil biota during the decomposition process. Differences in soil biology between soils from organic and conventional farming systems did not persist when soils were amended with organic matter and maintained under similar conditions. Microbial communities in soil from the conventional system were sufficient and active enough to respond to organic inputs. There were minimal differences in the ability of the microbial communities of the two soils to decompose organic residues. However, when soils were removed from the field at different times, cover crop decomposition rates were more consistent in the organic soils, suggesting a greater abundance and diversity of the microbial community in those soils. Microbial activity was most suppressed when field soils were dry but responded to organic matter amendment very rapidly when favorable moisture contents were restored. The pattern of microbial activity in both organic and conventional soils following organic matter incorporation consisted of a 100 h activity phase and then a gradual decline to a relatively constant stasis phase.