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Application of organic residues to soil is generally assumed to improve soil tilth. Only few studies have reported the long‐term effects on the more subtle aspects of soil porosity, and no reports have considered the potential effects of organic amendments on the pore system in the subsoil. We sampled undisturbed soil cores (100 cm³ and 6280 cm³) using metal cylinders in differently fertilized plots in the long‐term field experiment at Askov Experimental Station, Denmark. We selected the 0–60 cm soil layer of plots dressed for a century with either mineral fertilizers (labelled NPK) or animal manure (labelled AM) and unfertilized plots (UNF) as a reference. Both fertilization treatments were studied at two levels of nutrient application: ‘normal’ (labelled ‘1’) and 1.5 times ‘normal’ (labelled ‘1½’). Water retention, air permeability and air diffusivity were measured on the small cores, and we used the large cores for …