Water erosion is the most important degradation process affecting Epicalcic Chernozems quality. Many technologies and tillage systems are used to control water erosion in agricultural areas and to preserve soil fertility. Cover crops are considered an agricultural practice that contributes to carbon sequestration, improved infiltration, erosion control, and improved microbiological processes. The aim of the present study was to determine how the continuous application of a cover crop, in a wheat-maize rotation on sloped arable land, would alter the soil organic carbon, greenhouse gas fluxes and the soil microbial community, as the most significant regulator of soil carbon dynamics and biogeochemical cycles. An experiment with wheat and maize, in rotation, with the application of up-and-down slope culture (T0), traditional contour tillage (T1) and crop specific erosion control contour tillage (T2) was performed for four years in the experimental field Trastenik, Ruse. The T2 variant includes minimum tillage, direct sowing and cover crop after wheat harvest and before maize sowing. The content of total organic carbon, labile organic matter, the number of main groups of soil microorganisms, as well as CO2 and N2O soil emissions were monitored. In comparison to T0 and T1 treatments, an increasing number of ammonifying, cellulose decomposers, actinomycetes, and nitrogen-fixing bacteria were determined in the T2 variant under maize. In the spring and summer, there were higher number actinomycetes and cellulose decomposers in wheat variants. The enhanced total organic carbon was determined in T2 treatments. Soil CO2 emissions (29.8 kg ha-1 day-1) were reduced in the minimum tilled wheat variant, followed by the T0 (30.0 kg ha-1 day-1) and T1 (30.8 kg ha-1 day-1). The soil crust formation due to more intensive erosion process explains the lower average emissions under maize at the T0 variant, grown conventionally up and down the slope in comparison with T1 and T2. N2O emissions were generally lowest in the T2 treatments for both crops in four years. The minimum tillage for maize and wheat growing on slope lands with the inclusion of cover crop in the rotation, have a positive effect on soil organic matter, microflora and GHG emissions.