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Abstract Eucalyptus trees grow in a variety of environmental conditions and cause contrasting effects on soils. Changes in soil geochemistry and mineralogy due to eucalyptus have not been clearly established to date. The objective of this study was to identify evidences of the effects of eucalyptus root system on geochemistry and clay mineralogy of a Ferralsol. Soil samples were collected in different positions of an old eucalyptus site (R1: rhizosphere of small roots; R2: coarse roots, and R3: bulk soil). The soil pH was very acid (3.8) and Al3+ (4.7 cmol c kg−1) and H+ + Al3+ (40.2 cmol c kg−1) were higher in R1 compared to R3. Additionally, reduction of clay fraction content and an increase in the proportion of Al-interlayered clay minerals were also observed in the eucalyptus rhizosphere. This suggests the occlusion of Al3+ in the interlayer space of 2:1 clay minerals and explains the tendency of a low cation exchange capacity of the clay fraction. Then, the acidification due to eucalyptus did not alter the composition of the mineral assemblage (mineral species) but the trend was a decrease of the proportion of the fine clay fraction (<0.1 μm) as well as an increase of the proportion of 2:1 Al-interlayered clay mineral in the clay fraction. The results suggest that when alien tree species are introduced into natural lands worldwide, a comprehensive geochemical-mineralogical approach must be applied in order to provide the extension of constituent changes. Highlights • Soil samples from eucalyptus rhizosphere were compared in their geochemical and mineralogical aspects with bulk soil. • The low soil pH condition in the rhizosphere of eucalyptus resulted in soil acidification and clay dissolution. • Clay dissolution increased Al3+ contents, increasing the formation of hydroxy-Al interlayered clays. [ABSTRACT FROM AUTHOR]