NanoSIMS (Nanoscale Secondary-Ion Mass Spectrometry) is a powerful analytical technique that allows quantitative, subcellular imaging of incorporation and transfer of isotopically labeled compounds and metabolites in biological tissue (Hoppe et al., 2013). This technique is well adapted to study small organisms such as foraminifera. Recent studies have successfully applied NanoSIMS analysis of foraminifera to study the localization of labeled compounds incorporated into their calcium carbonate test and into the cell itself. In the test, it was applied to better understand the microdistribution of different elements (e.g. Mg/Ca ratio) used as proxies for paleoclimate reconstruction (e.g. Kunioka et al., 2006; Nehrke et al., 2013; Tachikawa et al., 2013). One study correlated NanoSIMS with TEM imaging to study the incorporation of isotopically labeled nitrate and sulfate in benthic foraminifera cell (Nomaki et al., 2016). In a series of individual experiments, we have used NanoSIMS in combination with TEM to study metabolic processes in foraminifera: 1) Heterotrophic feeding was investigated in the benthic species A. tepida under oxic and anoxic conditions (Lekieffre et al., 2016). 2) The spatio-temporal dynamics of assimilation and translocation of 13C-bicarbonate and 15N-ammonium/nitrate was investigated in both benthic (kleptoplastidy) and planktonic (symbiotic) foraminifera with pulse-chase experiments. In a benthic species containing sequestered chloroplasts, these were demonstrated to play a significant role in the incorporation of both inorganic carbon and nitrogen into the cytoplasm (Jauffrais et al., 2016 TMS oral presentation). Symbiotic planktonic foraminifera showed rapid uptake of bicarbonate and ammonium through the symbionts, whereas uptake of nitrate was less efficient.