Second Miocene Seam Complex (2nd MFK; germ.: 2. Miozäner Flözkomplex) holds many in-situ, not permineralised fossil tree stumps and trunks with high-cellulose contents. The state of preservation of a set of in-situ fossil trees (Taxodioxylon cryptomerioides, Sciadopityoxylon wettsteinii, and Quasisequoioxylon piskowitzense) collected from three open-cast mines (Welzow-Süd, Meuro, and Piskowitz) in Lusatia lignite mining district, Federal Republic of Germany was investigated using a multi-method research schema. Examination of preservation state of thermally immature fossil woods revealed: (1) well-preserved (non-deformed, non-degraded, and non-flattened) textinite, (2) a retained structural integrity represented by multilayered (multi-zoned) cells with primary, secondary cell wall, and middle lamella, (3) microfracturing restricted to secondary walls only, (4) preservation of polyphenolic parenchyma cells (PP cells), (5) excellent preservation of pits in ray tracheids, (6) presence of amorphous silica (opal-A) coating, and (7) crystalline silica (opal-CT) fillings of small-bladed crystals. Thermogravimetric analysis results showed dissimilar gelification status of fossil samples, supporting chlorite holocellulose assay results. The latter indicated anomalously high-cellulose values (15.6–37.6% holocellulose). The micro-FTIR data obtained revealed an excellent preservation of both hemicellulose (bands at 1740 and 1245 cm−1) and cellulose (bands at 1110 and 1040 cm−1). Micro-FTIR spectrometry indicated lack of preferential hydrolytic removal of polysaccharides in examined samples. Biomarker patterns in lignite revealed forested and prevailing reed-mire vegetation. The results indicated lower contribution of Cupressaceae and emergent macrophyta to precursor organic matter of Welzow-Süd in comparison to Piskowitz lignite. Piskowitz lignite formed in permanent mire with stable water table under reducing, mesotrophic conditions. In contrast, more pronounced water level fluctuations (reducing to slightly oxic settings) and/or post-depositional events are postulated for Welzow-Süd samples. Biomarker assemblages obtained from fossil wood show a distinct dominance of diterpenoids and δ13C values (−24.6 ‰ to −20.3 ‰) that clearly confirm gymnosperm sources. Distributions of diteprenoids and sesquiterpenoids, as well as fatty acids indicate the higher amount of saturated diterpenoids (pimarane, abietane) in fossil than in modern wood. This indicates reducing conditions promoting hydrogenation reactions. In addition to low Eh, preservation of cellulose in fossil wood was also favored by acidic conditions, very low degrees of aerobic fungal degradation, and protection of wood by Cupressaceae-derived resins. While δ13C values of fossil wood are generally consistent with stratigraphic trends and chemotaxonomical classification, slightly elevated δ13C values recorded in T. cryptomerioides and S. wettsteinii in Welzow-Süd and Meuro open-cast mines, respectively, compared to published δ13C data of fossil gymnosperm wood are also indicative for good cellulose preservation. Both preservation of in-situ Miocene fossil stumps and trunks and retention of high-cellulose contents are suggested to be related to high-amplitude temporal fluctuations associated with repeated eustatically-controlled wet-dry cycling inducing: (1) weathering of tuff- and rhyolite-dominated acidic volcanics and Lausitz granodiorite, (2) associated erosion of saprolites, and (3) peat-sourced circulation of humic acid- and fulvic acid-rich waters. The latter led to the formation of Middle Miocene kaolinite deposits, as well as to the release of silicic acid and its subsequent precipitation in form of opal-A. The latter influenced preservation of high-cellulose contents in fossil wood.