Organically managed (ORG) soil is often considered healthier than conventionally managed (CONV) soil, with greater resistance and resilience to disturbances, as evidenced by reduced oscillations in bacterial populations and activities. Greenhouse gas (GHG) fluxes are mediated by bacterial processes, but variations in GHG emissions have not been related to bacterial oscillations in soil. Two environmentally controlled and two field experiments were set up to compare oscillations in bacterial colony-forming-units (CFUs) and GHG (nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4)) fluxes after disturbances in ORG and CONV soils. Soil amendment with grass-clover (GC) or cattle manure (CM) resulted in peaks in N2O and CO2 emission, followed by CFUs. CH4 temporarily increased in GC- but decreased in CM-amended soil. Ratios of CFUs and GHGs in amended over nonamended soils oscillated during three weeks, mostly with lower frequencies and amplitudes in ORG soils. Fluctuations were more irregular in field soils, but significant oscillations were detected after irrigation or intensive rain in summer. Cross correlations between variables showed several significant sequences of microbial processes under controlled conditions but not in the field. Average GHG emissions were higher from ORG soil than CONV soil under these conditions, indicating that these have to be taken into consideration when estimating soil health.