Conservation agriculture is increasingly preferred to conventional methods due to its benefits in promoting more sustainable soil management. Our study aims to compare physical and morphological properties, at the microscale, of soils under long-term no tillage (NT) and minimum-tillage (MT) to adjacent ‘natural’ soils under long-term secondary forest (SF). Soil aggregates of c. 2 cm length were imaged by X-ray Computed Tomography (XCT). The three-dimensional (3D) images were segmented and analyzed in order to assess properties such as porosity, number of pores, degree of anisotropy, pore shape, volume classifications, Euler number for pore connectivity, and pore tortuosity. The pore architecture of soils under NT and MT, for c. 40 years, was similar to that from the SF in terms of imaged porosity, pore size, and shape distributions, as hypothesized in our study. However, we observed some important differences; for instance, SF had larger, more connected, and more complex pores, likely due to the greater biological activity. In addition, SF had more isotropic pores than NT and MT, i.e., without preferential flow paths for water redistribution. Therefore, we concluded that long-term conservation agriculture was efficient at reversing structural damage typically associated with conventional, intensive agriculture, but some large differences remain, particularly concerning the pore network complexity and connectivity.