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Data are related to Confocal Laser Scanning Microscopy (CLSM) observations of lipid-enriched Chlamydomonas reinhardtii cells under different conditions. Firstly, the impact of stress conditions (nitrogen starvation) on the cell wall structure is assessed. Secondly is described the effect of solvents, in the context of lipid extraction, on the microalga's cell, particularly its lipid droplets, in the perspective of understanding the mechanisms behind solvent extraction of lipids. Furthermore, the role of the cell wall as a barrier to the solvent extraction action is highlighted.