Direct observations of processes occurring at the mineral-organic interface are increasingly seen as relevant for the cycling of both natural soil organic matter and organic contaminants in soils and sediments. Advanced analytical tools with the capability to visualize and characterize organic matter at the submicrometer scale, such as Nano Secondary Ion Mass Spectrometry (NanoSIMS) and Scanning Transmission X-ray Microscopy (STXM) coupled to Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS), may be combined to locate and characterize mineral-associated organic matter. Taking advantage of samples collected from a decadal N-15 litter labeling experiment in a temperate forest, we demonstrate the potential of NanoSIMS to image intact soil particles and to detect spots of isotopic enrichment even at low levels of N-15 application. We show how microsites of isotopic enrichment detected by NanoSIMS can be speciated by STXM-NEXAFS performed on the same particle. Finally, by showing how N-15 enrichment at one microsite could be linked to the presence of microbial metabolites, we emphasize the potential of this combined imaging and spectroscopic approach to link microenvironment with geochemical process and/or location with ecological function.