In the last 250 years the Aquands (depth-limited and waterlogged-volcanic ash soils) in southern Chile were exposed to an intensive land use change inducing physical degradation of these fragile soils. The aim of this work was to evaluate the effect of cyclic loading on soil structural properties and the resilience capacity after simulating one event of soil waterlogging as usually occurs in the field. In undisturbed soil samples, collected from two horizons (2−5 cm, Hz1 [A1] and 20−23 cm, Hz2 [Bs1]) of a Duric Histic Placaquand under secondary native forest (sNF) and naturalized grassland (NG), the precompression stress (Pc), deformation and recovery indices derived from cyclic loading tests (20, 80 and 200 kPa) were determined. The air permeability (Ka) and soil volume changes were measured during the entire test. The land use change from sNF to NG increased the rigidity of the pore system due to plastic deformation. However, the cyclic loading provokes changes in the pore system (e.g. increase in bulk density as well as decrease in wide coarse pores, which finally induce a decrease in air permeability: 1.89 to -0.17 log μm2 and 1.03 to 0.37 log μm2 in Hz1 of aNF and NG, respectively) even at loads lower than Pc highlighting the fragility of the soils. As the applied load increases to levels higher than Pc, the plastic deformation induces an increase in pore water pressure and mechanical strength, affecting the pore network and in turn the air permeability of the soil. After one event of ten days of waterlogging conditions, the resilience capacity of the pore system was low. CT-images show that the soil under sNF recovered apart of the deformed porosity allowing an increase in Ka (0.55 ± 0.15 log μm2) after waterlogging conditions, however, no changes were identified for the soil under NG (final Ka = 0.57 ± 0.26 log μm2). Therefore, both land use change and increasing loads on these fragile soils imply the loss of their resilience capacity generating a further soil settlement.