The aim of this mini-review with own results was an identification of techniques to suppress the growth of microbial contaminants under photo- and mixotrophic conditions. Techniques identified are the modification of environmental conditions, such as pH, oxygen, and nutrient concentrations, as well as the application of pulsed electric field, ultrasonication, and surfactants. In phototrophic cultivations, the mentioned techniques result in a decrease of number of predatory cells, but not in a complete removal. Measures to suppress the growth of contaminations (e.g., bacteria and fungi) in mixotrophic cultivations could not be identified. The co-cultivation of algae and fungi, however, was found to be beneficial for the utilization of unusual carbon compounds (e.g., phenolic compounds).