Fossils that provide three-dimensional anatomical detail are among the most spectacular and significant archives of past life. However, the duration and speed of tissue mineralization often remain obscure, as do the sources of the fossilizing agents. We present a novel approach to reconstruct the deep-time 3D silicification of plant tissues, using Late Pennsylvanian fossil wood from fluvial red beds of the Kyffhäuser (Siebigerode Formation, Saale Basin, central Germany). Methods applied include fossil-wood histology, sediment petrography, cathodoluminescence (CL), scanning-electron microscopy, Raman spectroscopy, electron-probe and fluid-inclusion microanalysis, LA-ICP-MS in-situ U-Pb dating and Si isotopy of silicified fossil wood. The results reveal a 200-myr history of mineralization that occurred in concert with regional basin evolution. Accordingly, initial permineralization through amorphous silica is dated to 304±10 Ma and sourced from pyroclasts related to syndepositional, late-Variscan volcanism. This stage was followed by the opal-quartz transformation during subsidence until c. 290 Ma (early Permian). Around 260 Ma, hydrothermal quartz-hematite mineralization impacted the woods following middle–late Permian inversion. Blocky quartz sourced from basinal brines crystallized in the fossil trunks during maximum burial between 180–160 Ma (Late Jurassic), at 3.5–5.0 km depth and 160–240°C. The youngest mineralization found in the trunks dates to 115 Ma (Early Cretaceous) and resulted from regionally traceable, hydrothermal quartz-baryte-calcite mineralization in the course of inversion in the Central European Basin System. These outcomes not only break new ground in understanding cell-scale fossilization but also reveal silicified plants as promising tools for reconstructing basin evolution and regional mineralization.