Biogeochemical interfacial associations and processes, are crucial for many environmental and earth systems, including soils, sediments, biominerals, biofilms. In this context, associations of organo-mineral and microbial-mineral, involving organic and biologic materials and clay minerals and Fe- and Al-(hydr)oxides, and redox processes of Fe and other active metals, such as Mn, Ni, Cu, are highly entangled and interrelated. Their highly heterogeneous nature in physics, chemistry, structure and biology makes it very challenging to be fully characterized and understood. Synchrotron soft X-rays based spectromicroscopies, specifically the scanning transmission X-ray microscopy (STXM) and its technique and method developments, coupled with the X-ray Absorption Near Edge Structure (XANES) spectroscopy, are well equipped to perform multi-element chemical speciation and quantitative chemical imaging in 2D and 3D, identification of organic and inorganic components and their associations, and spatial correlation analysis of elements, at high spatial resolution (10 to 30 nm) and high spectral resolution (< 0.05 eV). In this presentation, spatially-resolved multi-element chemical analysis of selected environmental and earth samples with respect to biogeochemical interfacial associations and processes using STXM will be presented. In addition, recent STXM instrumentation developments, such as XRF-STXM, in vivo 3D STXM, will also be covered to show the strong capabilities and potentials of STXM characterizations.