Phytoliths are microscopic structures made of amorphous opal (opal-A), an amorphous hydrated silica, dispersed within plant tissues and persisting after the decay of the plant. Silicon is known to alleviate metal toxicity in plants, but the role of phytoliths in metal sequestration and detoxification is unclear. Dry ashing, the most common protocol for phytolith extraction, was previously shown to lead to sequestration of metals by the phytoliths; however, the mechanisms of this process remained elusive. The purpose of this study was to evaluate whether the association between metals and phytoliths results from dry ashing or pre-exists in plant tissues. Thus, we compared phytoliths extracted by dry ashing at 700 °C and plant leaves before and after dry ashing. A combination of ICP-MS, XRD, SEM-EDX and Zn-K-edge EXAFS spectroscopy was used to assess elemental concentrations, morphology and crystallography of silica, and chemical status of Zn. Results demonstrated a phase transition from amorphous opal (opal-A) to opal-CT and α-cristobalite, and the sequestration of metal in phytoliths during dry ashing. For Zn, Mn and Pb, a linear relationship was found between the concentration in phytoliths and in leaves. In the phytoliths, Zn was sequestered in silica in tetrahedral configuration. We hypothesize that this association results form a solid-state reaction during ashing, involving a redistribution of Zn from the organic material to the silica, possibly promoted by the release of structural water from amorphous opal throughout the heating procedure. This study improves our understanding of the impact of high temperature treatments on plant biomass and phytoliths. It suggests that Zn toxicity alleviation in plants by silicon does not rely on its sequestration by phytoliths. In natural settings, wild fire events and biomass burning may lead to metal sequestration in low-soluble form, which should be considered in modeling of biogeochemical cycles and in paleoenvironmental studies.