A range of indicators including chemical, physical, morphological, and clay mineral properties were investigated to support an integrated evaluation of the changes induced by a long established olive grove on a red Mediterranean soil. The study area was located in Sardinia (Italy). Two soil profiles were studied in a site where land use had remained unchanged for the previous 150 years: one under the canopy and around the trunk of an olive tree and one between the trees. Chemical analyses including organic matter fractions were performed by horizon. Undisturbed soil samples were collected from aggregates for thin section and scanning electron microscopy (SEM) analyses, complemented by clay mineralogy. Relative compaction was observed in tree topsoil due to the pressure of the anchoring roots. Lower compaction, higher porosity, and less developed micro-aggregates were observed in deeper horizons in relation with the loosening action induced by roots. Sharper vertical chemical gradients were determined under the tree. Stress features were observed in thin sections from all the horizons. Traces of smectite were determined as indicator of past shrink-swell processes suggesting that the present-day dominance of illite-like minerals might be explained by transformation of smectite induced by pedogenesis and by the long-lasting K-enriching action of the plants. Our findings indicate the need to undertake more systematic, integrated, and comparative future research on this subject.