Non-concentrated algae storage can bridge the period between algae harvesting and processing while avoiding the stress conditions associated with the concentration step required for concentrate storage. This study aimed to examine organic matter losses during the non-concentrated storage of Microchloropsis gaditana at pilot-scale. Algae cultures (400–500 L) were stored for up to 12 days either at an 8 °C target temperature or at 19 °C as the average temperature. The centrifugation yield of stored algal cultures decreased from day 5 or day 8 onwards for all storage conditions. After 12 days, the centrifugation yields were between 57% and 93% of the initial yields. Large differences in centrifugation yields were noted between the algae batches. The batch-to-batch difference outweighed the effect of storage temperature, and the highest yield loss was observed for the 8 °C cooled algae batch. The analysis of stored algae before and after centrifugation suggested that the decreasing yields were not related to respiration losses, but rather, the decreasing efficiency with which organic matter is collected during the centrifugation step.