The study presents the impact of management practices on greenhouse gas emissions (GHG) and nitrogen (N) losses calculated with a denitrification-decomposition model. Two cropping systems were analysed. The first rotation (A) consisted of potato, winter wheat, spring barley and corn. The second (B) included potato, winter wheat, spring barley and clover with grasses mixture. In A1 and B1 scenarios, fluxes were estimated on the basis of mineral fertilizers input, whereas in A2 and B2 scenarios the assessment of emissions was made with regards to manure. The results indicated that the application of manure in A rotation led to the increase of nitrous oxide (N 2O) emission, N leaching, N surplus, crop yields, and the decrease of nitrogen use efficiency higher than in B rotation. Additional doses of manure in A2 scenario increased the potential of the accumulation of soil organic carbon (SOC) and global warming potential (GWP) by 157%. In B2 scenario, SOC augmented more than three-fold but GWP increased only by 10%. The N losses and GHG emissions could be minimised by controlling N application through the implementation of nutrient management plan in which N doses are defined based on the crop needs and soil quality.