In oxygenic phototrophs including unicellular algae, acclimation to and damage by diverse environmental stresses induce profound changes in the ultrastructural organization of the cell. These alterations reflect acclimation of the photosynthetic apparatus to unfavorable conditions (mainly reduction of the chloroplast and its membranal system) and rewiring of the photo‐fixed carbon fluxes in the cell. These changes, eventually pursuing mitigation of the photooxidative damage risk, are manifested by the formation of diverse carbon‐rich inclusions. Although the physiological and molecular basis of these processes are well understood, the ultrastructural manifestations of the stress responses are often fragmented and frequently controversial. This minireview attempts to generalize on the ultrastructural patterns accompanying stresses in the photosynthetic cell, involving the concerted rearrangements of its assimilatory and storage compartments. The changes characteristic of normal functioning and emergency reduction of the chloroplast thylakoids under harsh stress are also addressed. Special attention is paid to the manifestations of the engagement of photoprotection via active (energy‐dependent non‐photochemical quenching) and passive mechanisms (e.g. optical shielding by secondary carotenoids). We also underline the potentially important role of autophagy‐like processes and provide a more integral view of ultrastructural rearrangements under stress.