Abstract Mechanical disturbance of soil structure is commonly related to altered physical changes in pore systems, which control CO 2 effluxes e.g. by changes in gas transport properties and in microbial activity. Soil compaction mostly leads to reduced CO 2 fluxes. In contrast, structured soils can also release physically entrapped CO 2 or give access to protected carbon sources inside aggregates due to aggregate breakdown by disruptive forces. In this study it was investigated how far arable soil management affects structure- and compaction-related CO 2 -releases using incubation experiments and CO 2 gas analysis under standard matric potentials (−6 kPa). CO 2 efflux was analyzed before, during and after mechanical loading using the alkali trap method (static efflux) and a gas flow compaction device (GaFloCoD, dynamic efflux). Intact soil cores (236 and 471 cm 3 ) were collected from a Stagnic Luvisol with loamy sand (conservation and conventional tillage systems) and a Haplic Luvisol with clayey silt (under different fodder crops) from the topsoil (10–15 cm) and subsoil (35–45 cm). Mechanical stability was reflected by the pre-compression stress value (P c ) and by the tensile strength of aggregates (12–20 mm). Changes in pore systems were described by air conductivity as well as air capacity and total porosity. While CO 2 -releases varied highly during the compaction process (GaFloCoD) for different stress magnitudes, soil depths and management systems, basal respiration rates were generally reduced after mechanical loading by almost half of the initial rates irrespective of soil management. For both methods (dynamic and static efflux) restriction in gas transport functionality was proved to have major influence on inhibition of CO 2 efflux due to mechanical loading. GaFloCoD experiments demonstrated that decreases in CO 2 efflux were linked to structural degradation of pore systems by exceeding internal soil strength (P c ). Otherwise, re-equilibrating matric potentials to −6 kPa and re-incubating offset inhibition of soil respiration suggest a re-enhancement of microbial activity. At this state, physical influences were apparently overlapped by biological effects due to higher energy supply to microbes, which could be offered by spatial distribution changes of microorganisms and organic substrates within a given soil structure. This implies the susceptibility of physical protection mechanism for carbon by disruption of soil structure. In future, special focus should be given on a clear distinction between physical and microbiological effects controlling CO 2 fluxes in structured soils.