In soils, silicon released by mineral weathering can be retrieved from soil solution through clay formation, Si adsorption onto secondary oxides and plant uptake, thereby impacting the Si-isotopic signature and Ge/Si ratio of dissolved Si (DSi) exported to rivers. Here we use these proxies to study the contribution of biogenic Si (BSi) in a soil–plant system involving basaltic ash soils differing in weathering degree under intensive banana cropping. δ 30Si and Ge/Si ratios were determined in bulk soils (<2 mm), sand (50–2000 μm), silt (2–50 μm), amorphous Si (ASi, 2–50 μm) and clay (<2 μm) fractions: δ 30Si by MC–ICP–MS Nu Plasma in medium resolution, operating in dry plasma with Mg doping (δ 30Si vs. NBS28 ± 0.12‰ ± 2 σ SD), Ge/Si computed after determination of Ge and Si concentrations by HR–ICP–MS and ICP–AES, respectively. Components of the ASi fraction were quantified by microscopic counting (phytoliths, diatoms, ashes). Compared to fresh ash (δ 30Si = −0.38‰; Ge/Si = 2.21 μmol mol −1), soil clay fractions (<2 μm) were enriched in light Si isotopes and Ge: with increasing weathering degree, δ 30Si decreased from −1.19 to −2.37‰ and Ge/Si increased from 4.10 to 5.25 μmol mol −1. Sand and silt fractions displayed δ 30Si values close to fresh ash (−0.33‰) or higher due to saharian dust quartz deposition, whose contribution was evaluated by isotopic mass balance calculation. Si-isotopic signatures of bulk soils (<2 mm) were strongly governed by the relative proportions of primary and secondary minerals: the bulk soil Si-isotopic budget could be closed indicating that all the phases involved were identified. Microscopic counting highlighted a surface accumulation of banana phytoliths and a stable phytolith pool from previous forested vegetation. δ 30Si and Ge/Si values of clay fractions in poorly developed volcanic soils, isotopically heavier and Ge-depleted in surface horizons, support the occurrence of a DSi source from banana phytolith dissolution, available for Si sequestration in clay-sized secondary minerals (clay minerals formation and Si adsorption onto Fe-oxide). In the soil–plant system, δ 30Si and Ge/Si are thus highly relevant to trace weathering and input of DSi from phytoliths in secondary minerals, although not quantifying the net input of BSi to DSi.