Foraminifera are ubiquitous eukaryotic protists inhabiting all types of marine environments. The chemical and isotopic compositions of their carbonate tests are commonly used as proxies for paleo-environmental conditions. However, while foraminifera represent a large fraction of the meiofauna and could therefore play a significant role in biogeochemical cycles, little is known about their biology. For the last 30 years, studies have revealed a wide range of physiological functions and metabolic pathways, in both planktic and benthic foraminifera: symbiosis, denitrification, kleptoplasty, dormancy, etc. However, the detailed metabolic processes involved in this large variety of physiological functions remain poorly understood. NanoSIMS, the main analytical technique used in this work, is a powerful analytical technique to simultaneously visualize, with a high spatial resolution (ca 100 nm), and quantify the incorporation of isotopically labeled compounds in organisms. In this study, NanoSIMS was combined with TEM to investigate the spatio-temporal dynamics of isotopically labeled compound assimilation at a sub-cellular scale. The first chapter presents an inventory of TEM pictures of the main organelles found in benthic foraminifera based on the literature, complemented by new TEM observations of nine benthic species. This work is essential to interpret the data of the chapters that follow. Using NanoSIMS combined with TEM, the second chapter investigates the heterotrophic metabolism, under oxic and anoxic conditions, of the intertidal benthic foraminifera, Ammonia cf. tepida. A sharp decrease of the metabolic activity observed in anoxia strongly suggests dormancy in response to the lack of oxygen. The third chapter is dedicated to kleptoplasty in benthic species. Incubation with labeled 13C-bicarbonate, 15N-ammonium, and 34S-sulfate were made, and the assimilation and fate of these molecules and their metabolites within the foraminiferal cell were traced with correlated TEM-NanoSIMS. A number of key observations were made: (1) assimilation of inorganic C was shown in the kleptoplastic Haynesina germanica under light conditions, but was not observed under dark conditions, indicating a photosynthetic uptake via the kleptoplasts. (2) In a different species, Elphidium williamsoni, photosynthetic assimilation of inorganic C was also observed, but the observed 13C-enrichments were much lower and not found in the same organelles as in H. germanica, indicating differences in the metabolic pathways among kleptoplastic species. (3) Assimilation of NH4+ and SO42- was documented in both kleptoplastic and akleptoplastic species, strongly suggesting the existence of a cytoplasmic pathway for NH4+ and SO42- assimilation. Thus, the role of kleptoplasts in N and S foraminiferal metabolism remains unclear and need further investigations. Finally the last chapter applied a similar protocol to study the C assimilation dynamics in symbiotic dinoflagellates and subsequent transfer the planktonic foraminiferal host cell. Dinoflagellates are transferring large amounts of photosynthates to the foraminifera, mainly in the form of lipid droplets. In conclusion, correlated TEM and NanoSIMS imaging is an efficient tool to study foraminiferal metabolism. Through this study it has led to progress in the knowledge of their ultrastructure and metabolic pathways, and ultimately shed light on their potential role in the biogeochemical cycles of marine ecosystems.