In this study, we used a DNA fingerprinting technique (PCR-DGGE) to investigate if bacteria present in an activated EM suspension (EM-A) were able to maintain or reach significant relative abundances after addition to slurry manure. We also investigated effects of the addition of EM-A to slurry manure on nitrogen losses from the manure and grass biomass production after application of the manure as organic fertilizer. EM® and Agri-mest® were tested in a factorial set-up so that the factors could be distinguished. Effective Organisms (EM) is a mixture of several effective, disease-depressing micro-organisms. Agri-mest contains energized minerals, which will influence biochemical processes occurring in the manure. Different EM-stocks, and EM-Active suspensions prepared by different users showed large variation in bacterial community structure and, thus, low reproducibility. Through the addition of Agri-mest to the slurry manure, loss of inorganic nitrogen from the slurry manure appeared to be reduced. Moreover, after application of such Agri-mest slurry as an organic fertilizer, nitrogen uptake by grass was reduced. Addition of EM-A had no measurable effects on the bacterial diversity and the chemical composition of the slurry manure. In a pot experiment, also no effects of EM on nitrogen uptake and grass biomass production were recorded.