The objectives of the study were to: (1) assess the strength of associations of direct CO2 and N2O emissions with the seasonal variations in the relevant soil properties under both tillage systems; 2) evaluate how CT and RT affect magnitudes of seasonal CO2 and N2O fluxes from soil. Field studies were carried out on plots for conventional tillage (up to 0.22–0.25 m) and reduced tillage (up to 0.10–0.12 m) during the growing season and post-harvest period of red clover. The results showed that daily CO2 emissions significantly correlated only with soil temperature during the growing season under conventional and reduced tillage. Soil temperature demonstrated its highest influence on daily N2O emissions only at the beginning of the growing season in both tillage systems. There were no significant inter-system differences in daily CO2 and N2O emissions from soil during the entire period of observations. Over the duration of post-harvest period, water-filled pore space was a better predictor of daily CO2 emissions from soils under CT and RT. The conventional and reduced tillage did not cause significant differences in cumulative N2O and CO2 fluxes from soil.