The temporary storage of wet algae concentrates enables the decoupling in time of algae harvests and their biorefinery. However, the impact of cultivation and of the harvest conditions on algae quality during preservation is largely unknown. This study aimed to determine the impact of nutrient limitation and of harvest methods on the preservation ofChlorella vulgarisbiomass. Algae were either well-fed until harvest or received no nutrients for one week, and were harvested by either batch or continuous centrifugation. The organic acid formation, lipid levels, and lipolysis were monitored. Nutrient limitation had a large impact and resulted in lower pH values (4.9 ± 0.4), high levels of lactic acid and acetic acid, and a slightly higher degree of lipid hydrolysis. Concentrates of well-fed algae had a higher pH (7.4 ± 0.2) and another pattern of fermentation products with mainly acetic acid, succinic acid, and, to a smaller extent, lactic acid and propionic acid. The effect of the harvest method was smaller, with, most often, higher lactic acid and acetic acid levels for algae harvested by continuous centrifugation than for those obtained by batch centrifugation. In conclusion, nutrient limitation, a well-known method to enhance algae lipid levels, can impact several quality attributes of algae during their wet storage.