Trace elements dynamics in the soil-plant system depends on multiple parameters, including chelating organic compounds from natural or synthetic organic matters. In this study, we evaluated the influence of one of the most common pesticides—glyphosate—on the mobility of trace elements considering contrasted soils (uncontaminated, anthropogenically contaminated, and naturally-enriched) in a greenhouse experiment. Four modalities have been tested: one control without any application, two with different glyphosate doses (1 and 3 times the authorised field dose), and one with compost addition to evaluate its potential ability to mitigate the impact of glyphosate on trace element mobility. Both, trace element and glyphosate concentrations were measured in the soil solutions and trace element contents were determined in plants at the end of the experiment. The results showed that, although glyphosate concentrations rapidly decreased in soil solutions, glyphosate application still influenced the transfer of trace elements to both soil solution (up to 12-times higher) and plant (up to 5.2-times higher). This influence was highly dependent on both the specific elements and the type of soils considered. For instance, in uncontaminated soils, glyphosate especially increased the mobilization of Mn, Co, Zn, Mo, and Pb to soil solution. This effect diminished of 2.5 times on average with increasing soil contamination. A similar trend was observed for the transfer of trace elements from soil to plant (i.e., on average 2.2-times lower in the most contaminated compared to the uncontaminated soil). However, in the naturally-enriched soil, opposing trends were noted between soil solutions and plants. The impact of compost addition on the transfer of trace elements to plants remains unclear: compost enhanced the transfer of trace elements to soil solution in uncontaminated and naturally-enriched soils likely due to trace element input through the compost, but decreased the transfer in anthropogenically-contaminated soils likely due to adsorption processes. Therefore, glyphosate could potentially increase the exposure of trace elements through food consumption and their transfer to the ecosystem, particularly in uncontaminated and weakly contaminated soils. In highly contaminated soils, compost could mitigate the glyphosate-induced enhancement of trace element mobility to soil solutions.