The chemical composition of soil represents to a large extent the primary mineralogy and geochemistry of the source bedrock, the effects of pre- and post-depositional weathering and element mobility, either by leaching or mineral sorting with the addition of secondary products such as clays. Agricultural soil in Europe (0–20 cm, 33 countries, 5.6 million km2) was sampled during the continental-scale soil mapping project (GEochemical Mapping of Agricultural and grazing land Soil - GEMAS). Total element concentrations were determined by wavelength dispersive X-ray fluorescence spectrometry. Bulk content of major elements (SiO2, TiO2, Al2O3, Fe2O3, MgO, CaO, Na2O, K2O, P2O5) in soil has been used to calculate weathering indices such as chemical index of alteration (CIA), reductive and oxidative mafic indices of alteration (MIA), the change in mass balance (τ calculation relative to immobile Nb) for soil derived from silicate bedrocks (granite, gneiss and schist) at the European continental-scale, which are useful tools for evaluating chemical weathering trends. The greatest variation of CIA values is exhibited by soil derived from granite, followed by soil derived from schist. The CIA results show clearly that Ca and Na are removed from agricultural soil (0–20 cm) during soil development. Geographical distribution of weathering indices shows that weak chemical weathering of agricultural soil samples, sourced from gneissic and granitic bedrock, occurs in the Fennoscandian Shield; intermediate chemical weathering in granite, schist and gneiss occurring in the Iberian Peninsula and France, and intense chemical weathering in schist sourced agricultural soil occurring in areas with intense rainfall and moderate temperature (Wales, England, Ireland and western Iberia). In addition, values of CIA and MIA, higher than those for standard rock compositions, suggest more active enrichment/depletion processes during soil formation and subsequent soil weathering/maturation. The range of the elemental mass transfer coefficient τ is wide for agricultural soil derived from gneiss and granite, and narrow for agricultural soil sourced from schist parent rocks. The weathering behaviour of chemical elements, assessed by using the τ mass transport model, suggests an order of susceptibility of K ≈ Na > Al > Fe > Ca > Mg > Ti. Weathering indices and gain-loss mass transfer coefficients, tested on agricultural soil samples, provide an insight to the weathering processes affecting the silicate parent rocks and their impact on soil development at the European scale. This can have further implications for evaluation of soil nutritional conditions and mitigating of soil erosion and deprivation.