Thraustochytrium striatum was selected as a model protist to test the possibility of protist granulation for its good potential of organic waste valorization. Initially, only a selective settling velocity of 9 m h−1 was applied in a sequential batch reactor (SBR) with minimal granulation progress after three months. After the famine condition was introduced into the SBR with a feast-to-famine duration ratio of 0.2 by extending the cycle time and lowering the initial substrate concentration while keeping the selective settling velocity unchanged, protist granules with spherical shape and smooth surface formed and were dominated in the reactor after another month. The average particle size of protist granules was 728 μm, 90 times greater than its planktonic counterpart. This study evidenced the culture-independent phenomenon of aerobic granulation. Also, the combination of a low feast-to-famine duration ratio with a selective settling velocity was found to be required for inducing successful protist granulation.