In many soil processes, including solute and gas dynamics, the architecture of intra-aggregate pores is a crucial component. Soil management practices and wetting-drying (W-D) cycles—the latter having a significant impact on pore aggregation—are two key factors that shape pore structure. This study examines the effects of W-D cycles on the architecture of intra-aggregate pores under three different soil management systems: no-tillage (NT), minimum tillage (MT), and conventional tillage (CT). The soil samples were subjected to 0 and 12 W-D cycles, and the resulting pore structures were scanned using X-ray micro-computed tomography, generating reconstructed 3D volumetric data. The analysis was conducted in terms of multifractal spectra, normalized Shannon entropy, lacunarity, porosity, anisotropy, connectivity, and tortuosity. The morphological and geometric properties of the soil pores indicated that W-D cycles did not cause significant changes across the management systems studied. Furthermore, multifractal analysis revealed that the porous systems exhibited fractal behavior rather than multifractality. The results demonstrate that, within the resolution limits of the microtomography analysis, pore architecture remained resilient to changes, despite some observable trends in specific parameters.