Agricultural practices are assumed to contribute significantly to the increase in atmospheric nitrous oxide (N2O) concentrations observed in the last decades, and they might influence the consumption of atmospheric methane (CH4) by soil. The aim of this study was to quantify the effects of management intensity, soil type, and frost periods on the emission of N2O and the consumption of CH4 in rotations in southern Germany. Fluxes of N2O and CH4 were monitored over 12 months, using a closed chamber technique. The extensively managed system was cropped to sunflower and fertilized with farmyard manure (12 t ha−1). The intensively managed field was planted with spring wheat and fertilized with a total of 190 kg N ha−1 given as calcium ammonium nitrate (30 kg N) and urea-NH4NO3 solution (160 kg N). Variation in the N2O emissions with time was extremely high, with flux rates ranging from 0 to 2700 μg m−2 h−1. The N2O fluxes were influenced by soil properties, management practices, and weather. The highest release rates were measured in the winter during thawing of the frozen soil. During the growing season, N2O emission was highest after heavy precipitation. No strong relationship was found between N2O emission rates and soil factors such as soil temperature, soil moisture, and soil nitrate content. Annual fluxes of N2O from the extensively managed field were 9.4 and 12.9 kg N2O-N ha−1 yr−1 for a sandy soil and a clay soil, respectively. Total N2O-N losses from the intensively fertilized field amounted to 9.6 kg ha−1 yr−1 for a silty soil with a tendency to waterlogging during wintertime and to 16.8 kg ha yr−1 for a loamy colluvial soil. Up to 46% of the annual N2O evolution was emitted during December and January when frost/thaw cycles induced extremely high N2O production. The application of urea-NH4NO3 solution significantly increased N2O emission rates. Of the 160 kg N applied, 2.9 kg N or 1.8% was lost as N2O within a period of 8 weeks. Rates of CH4-C uptake varied from 0 to 17 μg m−2 h−1. Soil temperature correlated positively and soil moisture correlated negatively with the CH4 consumption. Stepwise multiple linear regression, including these soil factors, explained up to 44% of the variation in CH4 fluxes. Annual CH4-C uptake was rather similar for the intensively and extensively managed Eutrochrepts, ranging from 348 to 395 g ha−1. Significantly higher CH4-C consumption of 567 g ha−1 yr−1 occurred in the colluvial soil (Typic Udifluvent). N fertilizers had no effect on the CH4 flux rates.