Abstract The recovery of soil structure following intensive crop production is essential to maintain good fertility and productivity. It is well known that some crops with specific deep rooting characteristics can improve subsoil structure, but few measurements exist on the time to recovery or direct impacts on gas transport on aeration status, thus we hypothesized that root influence on soil structure formation has a significant impact over aeration. This study examined how far three crops and their different root architectures influenced soil structure and aeration by their ability to generate biopores and cracks. Effects of three crops were investigated: (i) shallow roots (Festuca arundinacea, fescue), (ii) taproot-herringbone (Cichorium intybus, chicory) and (iii) taproot-multibranch (Medicago sativa, alfalfa). They were grown in a Haplic Luvisol in a field experiment near Bonn (Germany) during years 2007–2009. Air diffusion, air permeability and air-filled porosity were analyzed as a function of crop type, crop duration (one, two and three years of continuous cultivation) and soil depth. Results of the diffusion measurements were compared with Buckingham's and Penman's estimation functions with respect to continuity and tortuosity indices. At a depth of 75 cm, alfalfa showed more macroporosity than chicory and fescue with means of 13.6%, 2.5% and 3.4%, respectively, and at 90 cm means of 17.8%, 2.3% and 4.4%, respectively. Measurements showed decreasing gas diffusion with depth under chicory and fescue cultivation, whereas increasing diffusion with depth under alfalfa. At 90 cm depth alfalfa significantly improved diffusion with respect to chicory and fescue with means of 0.035, 0.014 and 0.009 respectively. Greater soil structure development under alfalfa was interpreted from higher tortuosity index. Under chicory, higher continuity and lower tortuosity of pores dominated the advective transport. Significant effects were observed after three years of cultivation, which suggests the time needed for structural changes. The structural changes observed are promising to extend these results to other soils with swell/shrink potential.