Imaging resource flow in soil-plant systems remains central to understanding plant development and interactions with the environment. Typically, subcellular resolution is required to fully elucidate the compartmentation, behavior, and mode of action of organic compounds and mineral elements within plants. For many situations this has been limited by the poor spatial resolution of imaging techniques and the inability to undertake studies in situ. Here we demonstrate the potential of Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS), which is capable of the quantitative high-resolution spatial imaging of stable isotopes (e.g. (12) C, (13) C, (14) N, (15) N, (16) O, (18) O, (31) P, (34) S) within intact plant-microbial-soil systems. We present examples showing how the approach can be used to investigate competition for (15) N-labeled nitrogen compounds between plant roots and soil microorganisms living in the rhizosphere and the spatial imaging of (31) P in roots. We conclude that NanoSIMS has great potential to elucidate the flow of isotopically-labeled compounds in complex media (e.g. soil) and opens up countless new opportunities for studying plant responses to abiotic stress (e.g. (18) O3, elevated (13) CO2), signal exchange, nutrient flow and plant-microbial interactions.