LA-ICP-MS (Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry), PIXE (Particle Induced X-ray Emision), µ-XRD (Micro X-ray Diffraction) and SEM (Scanning Electron Microscope) techniques are combined in molecular taphonomy research on soft tissue remains and substrata in fossil assemblage from the Late Cretaceous (Turonian) Múzquiz Lagerstätte, Coahuila, northeastern of Mexico. Skin, gills, digestive tract, blood vessel and muscle fiber show preserved features at cellular levels. The study also revealed bacterial and fungal cells with an exceptional preservation induced by autigenic biominerals such as flourapatite and calcite; this biomineralization of cells probably occurred by spontaneous reactions in supersaturated solutions. Soft tissue preservation represents an important source of microbial fossilization and this process is recognizable as a bio-inorganic pattern of tiny crystallites preserving the morphology of both microbes and soft tissues. Organic contents of muscle cells were replaced by phosphatized minerals. Fungal and bacterial cells, including extracellular polymer (EPS), were preserved as casts and moulds. Ultrastructural and biogeochemical analysis of the sedimentary rock matrix yielded significant data on the genesis of the limestone-marl laminar rhythmites of the Múzquiz fossil bearing strata, probably induced by diagenetic alteration, mainly as consequence of aragonite dissolution in the laminar interfaces. Biogeochemical analysis of fossil material showed a high concentration of Si, P, Ca, Fe and enrichment of Na, Mg, K , Cr, Mn, Zn, As, Sr and Ba, suggesting that such elements may be involved in the process of soft tissue preservation and could be used as fossil fingerprints. Trace metal content reveals a significant amount of S, V, Ni, Cu, Cd, Sb, Tl, Bi, Th and U. These can operate as paleoenvironmental markers in order to reconstruct the ancient conditions and simulate the Lagerstätten settings, having direct implications for ecosystems evolutionary studies.