ABSTRACT When environmental conditions change, microalgae can modulate the size of their macromolecular pools and their elemental composition in order to accommodate their nutritional and energetic demands. In this context, we evaluated how O2 levels and S starvation alter the resource partitioning in terms of organic and elemental composition in Chlamydomonas reinhardtii. The analysis of gene transcription, photosynthetic energy production and organic pool allocation allowed us to identify a two-phase cellular response related to external O2 concentration: (1) a short-term response where S starvation induced the expression of S starvation genes immediately after the start of the perturbation; (2) a long-term response that consisted of a drastic reduction of photosynthetic energy production and changes in C allocation following S deprivation, which was related to oxygen conditions. In anaerobic conditions, S starvation did not affect the pools of carbohydrates and lipids, whereas the protein pool decreased slightly over time. On the other hand, in aerobic conditions, S starvation modulated all organic pools: carbohydrates, lipids and proteins. We conclude that the energy levels produced by fermentation metabolism are not sufficient to sustain the acclimation process in C. reinhardtii; moreover, S availability affects C. reinhardtii more than do oxygen levels.