The high input of mechanical energy in common agricultural practice can negatively affect soil structure. The impact of compaction (P) and rotovation (R) on soil pore characteristics was compared with those in soil from untreated reference (U) plots of a loamy sand soil receiving for 14 yr, either only mineral fertilizer (MF) or, in addition, animal manure (OF). Undisturbed soil cores were taken from two separate fields in consecutive years at an identical stage in the crop rotation. We measured soil organic carbon (OC), soil microbial biomass carbon (BC), and hot‐water extractable carbon (Chot). Water retention, air permeability and gas diffusivity were determined at −100 hPa in both years and for a range of water potentials in one of the years. The continued addition of animal manure had increased OC, BC, and Chot compared with the soil receiving only mineral fertilizer. Soil under treatment OF had larger porosity than that from treatment MF. Treatment P eliminated this difference and significantly reduced the volume of macropores. This interaction between soil organic matter content and mechanical impact was also reflected in the gas diffusion data. Specific air permeability was mainly influenced by mechanical treatment. Modelling the diffusion data normalized to the inter‐aggregate pore space showed no significant treatment effects on pore‐connectivity, although there was a tendency of more water blockage in soil under treatment MF. More studies are needed to confirm this interpretation. Our studies indicate that organic manure increases soil porosity, but compaction reduces the related gas exchange effects to the level of compacted soils receiving mineral fertilizer.