Silicified Agathoxylon-type wood of Late Palaeozoic age was characterized by means of cathodoluminescence (CL) and LA-ICP-MS of the quartz mass, which was found to contain wakefieldite, characterized by electron-microprobe (EMP) analysis, Raman microspectroscopy and X-ray diffraction. Although former organic matter is almost absent, plant anatomy served as the template for the quartz mass texture. Two generations of quartz mass were distinguished; the large proportion of the silicified wood consisting of brownish α-quartz with a dark reddish CL emission, and the minor portion of whitish ‘leached’ wood with a short-lived (transient) blue CL. On the outer edge, a silicified texture of formerly slightly humified wood also emits a dark reddish CL. Likely the wood specimen has been fossilized and diagenetically altered in several steps. The marginal part had been humified (reductively degraded) before the initial stages of silicification. The LA-ICP-MS analyses revealed chemical differences in all three distinct parts. The quartz mass relatively enriched in REEs and As and giving the dark reddish CL is interpreted as a primary diagenetic mineral mass. Whitish zones relatively depleted in U and V, and enriched in Al, Li, Rb, Cu, and Sr producing the blue CL would then be a secondary diagenetic overprint. An EMP/WDS analysis identified As-rich xenotime-(Y) and a solid solution of wakefieldite–(Ce) and wakefieldite–(Y), which locally enclose individual silicified tracheids. Wakefieldite, identified in silicified plant tissue for the first time, was most likely formed as a secondary mineral during post-depositional diagenesis. The mineral diagenesis did not erase the original anatomy of the wood.