In this work, microalgae cultivation trials were carried out in a membrane bioreactor to investigate fouling when the cultures of Chlorellavulgaris were grown under mixotrophic, heterotrophic, and phototrophic cultivation regimes. The Chlorella cultures were cultivated in wastewater as a source of nutrients that contained a high concentration of ammonium. In mixotrophic cultivation trials, the results showed that the elevated contents of carbohydrates in the soluble microbial product and proteins in extracellular polymeric substances probably initiated membrane fouling. In this case, the highest protein content was also found in extracellular polymeric substances due to the high nitrogen removal rate. Consequently, transmembrane pressure significantly increased compared to the phototrophic and heterotrophic regimes. The data indicated that cake resistance was the main cause of fouling in all cultivations. Higher protein content in the cake layer made the membrane surface more hydrophobic, while carbohydrates had the opposite effect. Compared to a mixotrophic culture, a phototrophic culture had a larger cell size and higher hydrophobicity, leading to less membrane fouling. Based on our previous data, the highest ammonia removal rate was reached in the mixotrophic cultures; nevertheless, membrane fouling appeared to be the fundamental problem.