The domesticated marine microalga Diacronema lutheri is of great interest for producing various highly valuable molecules like lipids, particularly long‐chain polyunsaturated fatty acids (LC‐PUFA). In this study, we investigated the impact of phosphorus (P) and nitrogen (N) starvation on growth, carbon fixation (photosynthetic activity) and partitioning, and membrane lipid remodeling in this alga during batch culture. Our results show that the photosynthetic machinery was similarly affected by P and N stress. Under N starvation, we observed a much lower photosynthetic rate and biomass productivity. The degradation and re‐use of cellular N‐containing compounds contributed to triacylglycerol (TAG) accumulation. On the other hand, P‐starved cells maintained pigment content and a carbon partitioning pattern more similar to the control, ensuring a high biomass. Betaine lipids constitute the major compounds of non‐plastidial membranes, which are rich in eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. Under P and N starvations, EPA was transferred from the recycling of membrane polar lipids, most likely contributing to TAG accumulation.