Compaction can seriously degrade soil in modern agriculture. Soil that has been temporarily removed and stored is particularly sensitive to compaction when restored, although little is known about the structural changes in such soils under mechanical loads. We investigated the structural changes in a restored soil that had been gently cultivated for several years and then was trafficked by a heavy combine harvester, analysing the macro-pore structure by quantitative morphometry of three-dimensional microcomputed tomography images. Increased trafficking caused decreases in both the porosity and connectivity of the macro-pores. The fraction of spherical pores (and thus the convexity of the pore space) and the mean pore separation were increased. Trafficking had no clear effect on the orientation of pores. While the mean pore diameter tended to decrease, biopores were more stable than interaggregate pores originating from the packing of soil aggregates. This is relevant for the development of structural stability in restored soils, as the macro-pores consist mainly of interaggregate pores initially, whereas biopores develop and increase in proportion only gradually over time. Quantitative morphometry provides valuable morphological indices for the objective assessment of the macro-pore structure and changes induced by compaction.