Large-scale microalgae cultivations are increasingly used for the production of animal feed, nutritional supplements and various high-value bioproducts. Due to the process size and other limitations, contaminations of microalgae fermentations with other photoautotrophic microorganism are frequently observed. In the present study, we explored the applicability of 5-isobutyl-2,3-dimethylpyrazine for the removal of contaminating microalgae from industrial photobioreactors. In order to select a representative microbial population for susceptibility experiments, reactor samples were obtained from a multi-stage cultivation process. Assignments of 18S rRNA gene fragment amplicons indicated that Haematococcus, Chlorella, and Scenedesmus were the three most frequently occurring microalgae genera in the selected reactors. Following the isolation of representative algae cultures, susceptibility tests were conducted with the antimicrobial pyrazine. It was demonstrated that all isolated contaminants are highly susceptible to the bioactive compound. The highest tolerance towards the alkylpyrazine was observed with Scenedesmus vacuolatus; solutions with 1.66% (v/v) of the active compound were required for its deactivation. Further tests with the vaporized pyrazine showed consistent reductions in the viability of treated microalgae. This pilot study provides evidence for the applicability of a novel, nature-based alternative for bioreactor decontaminations.