Soil management alters physical, chemical and biological soil properties. Stress application affects microbiological activity and habitats for microorganisms in the root zone and causes soil degradation. We hypothesized that stress application results in altered greenhouse gas emissions if soil strength is exceeded. In the experiments, soil management dependent greenhouse gas emissions of intact soil cores (no, reduced, conventional tillages) were determined using two experimental setups; CO₂ emissions were determined with: a dynamic measurement system, and a static chamber method before and after a vertical soil stress had been applied. For the latter CH₄ and N₂O emissions were analyzed additionally. Stress dependent effects can be summed as follows: In the elastic deformation range microbiological activity increased in conventional tillage soil and decreased in reduced tillage and no tillage. Beyond the precompression stress a release of formerly protected soil organic carbon and an almost total loss of CH₄ oxidizability occurred. Only swelling and shrinkage of no tillage and reduced tillage regenerated their microhabitat function. Thus, the direct link between soil strength and microbial activity can be applied as a marker for soil rigidity and the transition to new disequilibria concerning microbial activity and composition.