Abstract The application of animal manure effluents in ag- riculture in combination with nitrification inhibitors should be beneficial for nutrient recycling, soil quality, plant productiv- ity, and greenhouse gas emission and offer economic advan- tages to make them an alternative to conventional fertilizers. The present study aims to estimate the effects of the addition ofbovine manure effluentalone or togetherwitha nitrification inhibitor (3,4-dymethylpyrazol-phosphate (3,4 DMPP)) on the microbial community dynamics in a Mediterranean soil in an incubation experiment over 28 days. The application of the bovine manure effluent increased respiration, microbial biomass carbon, fungal and bacterial growth, and enzyme activities and changed the microbial community structure evaluated by the phospholipid fatty acid pattern. Adding the bovine manure effluent together with the nitrification inhibitor, although partly negating the positive effect of the effluent on soil microbial activity, still resulted in higher or similar growth and activity as in the control. Our results indicate that the addition of the nitrification inhibitor 3,4 DMPP together with a bovine manure effluent could be a promising solution to control the animal manure effluent application effects on soil microbiological properties and mi- crobial dynamics, as well as counteracting direct inhibiting effects of 3,4 DMPP on the soil heterotrophic community.