Abstract and Technical Context This dataset provides the high-resolution tomographic and geochemical evidence for the permineralisation study of Baieroxylon cicatricum (Specimen CTES-PB 12337). The data supports the "Digital Tapho-geochemistry" framework, correlating 3D anatomical preservation with sub-micrometric mineralogical phases. 1. Micro-CT Acquisition (Bruker SkyScan 1273) Voltage/Current: 100 kV, 166 µA. Resolution: 10 µm voxel size. Content: The repository includes a general dataset (1,428 slices) and a priority ROI (114 slices) highlighting the most significant mineralised tracheids. An animated 3D fly-through (.gif) is provided for rapid spatial visualisation of high-density inclusions. 2. Geochemical Validation (Raman & SEM-EDS) Table S1 (Raman): Detailed peak assignments for α-quartz, moganite, and opal, including vibrational modes (ν) confirming multi-phase silicification. Table S2 (EDS): Quantitative elemental data highlighting an average Chromium concentration of 7.56 wt%, alongside Iron (Fe) and Uranium (U). Raw Data: Includes the ASCII spectral file (Spot 04) for full analytical transparency. Taphonomic Significance The coexistence of metastable silica (moganite) and transition metals suggests a complex diagenetic history influenced by hydrothermal fluid circulation and local fault zones in the Guairá Basin, Paraguay.