Carbon and nitrogen compounds in agroecosystems have attracted much attention in recent years due to their key roles in crop production and their impacts on environment quality and/or climate change. Since fertilization profoundly disrupted the C and N cycles, several mitigation and/or adaptation strategies, including the application of farmyard manure (FYM) and/or urease and nitrification inhibitors (UI and NI), have been developed. The aim of this study was to evaluate the contents of soil organic carbon and its fractions, the total and mineral forms of nitrogen, as well as CO2 and N2O emissions under mineral and organic fertilization with and without urease and nitrification inhibitors in a maize agroecosystem. A two-year field study was carried out on Cambisols (silt) in Poland. The experiment scheme included nine treatments: C (the control without fertilization), UAN (Urea Ammonium Nitrate), UAN+UI, UAN+NI, UAN+UI+NI, FYM with N mineral fertilizer base, FYM with N mineral fertilizer base+UI, FYM with N mineral fertilizer base+NI, and FYM with N mineral fertilizer base+UI+NI. It was found that treatments fertilized with cattle FYM were higher sinks and sources of C and N compounds in comparison to the UAN plots. The organic carbon, humic and humin acid, and total nitrogen concentrations, in contrast to ammonium and nitrate nitrogen, were not affected by the inhibitors added. Nitrification and urease inhibitors were effective in decreasing N2O emissions only in treatments that were exclusively applied with UAN and had no significant influence on CO2 emissions.