Soils are structurally heterogeneous across a wide range of spatio-temporal scales. Consequently, external environmental conditions do not have a uniform effect throughout the soil, resulting in a large diversity of micro-habitats. It has been suggested that soil function can be studied without explicit consideration of such fine detail, but recent research has indicated that the micro-scale distribution of organisms may be of importance for a mechanistic understanding of many soil functions. Current techniques still lack the adequate sensitivity and resolution for data collection at the micro-scale, and the question ‘How important are various soil processes acting at different scales for ecological function?' is therefore challenging to answer. The nano-scale secondary ion mass spectrometer (NanoSIMS) represents the latest generation of ion microprobes, which link high-resolution microscopy with isotopic analysis. The main advantage of NanoSIMS over other secondary ion mass spectrometers is its ability to operate at high mass resolution, whilst maintaining both excellent signal transmission and spatial resolution (down to 50 nm). NanoSIMS has been used previously in studies focussing on presolar materials from meteorites, in material science, biology, geology and mineralogy. Recently, the potential of NanoSIMS as a new tool in the study of biophysical interfaces in soils has been demonstrated. This paper describes the principles of NanoSIMS and discusses the potential of this tool to contribute to the field of biogeochemistry and soil ecology. Practical considerations (sample size and preparation, simultaneous collection of isotopes, mass resolution, isobaric interference and quantification of the isotopes of interest) are discussed. Adequate sample preparation, avoiding bias due to artefacts, and identification of regions-of-interest will be critical concerns if NanoSIMS is used as a new tool in biogeochemistry and soil ecology. Finally, we review the areas of research most likely to benefit from the high spatial and high mass resolution attainable with this new approach.