Kleptoplasty is the process by which an organism sequesters algal chloroplasts while discarding or digesting other algal components. This ability is encountered in different organisms, including benthic foraminifera. Among kleptoplastic foraminiferal species, Haynesina germanica and Elphidium williamsoni are two ubiquitous species found in intertidal mudflats. Albeit significant differences, their kleptoplast functionality has been clearly shown in terms of photosynthetic efficiency and inorganic carbon uptake. However, the intracellular pathways involved in the inorganic C-assimilation remained unknown and the kleptoplast role in N-uptake, although often suggested, still needs to be clarified. Here, we correlate transmission electron microscope (TEM) observations, NanoSIMS (nanoscale secondary ion mass spectrometry) analysis and isotopic labelling experiments (H13CO3- and 15NH4-) to investigate N and C-assimilation pathways at a sub-cellular level. Additionally, we compare the results observed on E. williamsoni and H. germanica with those observed on, Ammonia cf. tepida, a non-kleptoplastic species. TEM-NanoSIMS observations suggest two different fates for the C assimilated via the kleptoplasts, involving either fatty acids in H. germanica, and probably soluble molecules such as carbohydrates in E. williamsoni. Both kleptoplastic and non-kleptoplastic species were labelled in 15NH4-. The few 15N-enriched kleptoplasts in the kleptoplastic species suggest that they play a role in the N-assimilation; whereas, in the non-kleptoplastic species our results suggest the existence of alternative N-assimilation pathway(s) in benthic foraminifera. Furthermore, the different metabolites quantified in the foraminiferal cell (sugars, organic acids, fatty acids and amino acids) provide new insights and clarify metabolic pathways involved in C and N-uptake in benthic foraminifera.