The sugar industry has long faced challenges from microorganisms during production. Preventing sugar losses and microbial-related issues such as the formation of organic acids, gases like CO2 or H2, or slimy substances continues to be key concerns. Fortunately, process parameters such as high temperatures, low pH values and limited oxygen availability create unfriendly conditions for microorganisms, and antimicrobial agents have been developed to control microbial growth. However, a proactive approach would utilize the advantageous properties of microorganisms to break down undesirable substances and promote desirable ones. For example, acidic by-products from bacterial metabolism lower the pH and thus stabilize sugar beet cossettes during pressing. Additionally, beneficial metabolic processes have been recognized, such as preferentially utilizing monosaccharides instead of sucrose or selectively degrading undesired substances (e.g., converting nitrite into elemental nitrogen). Modern sequencing techniques continue to identify unknown bacteria with the potential to improve the process. Exploring these bacteria could offer valuable insights for a better microorganism management in beet sugar production. This perspective article discusses the microbial diversity in beet sugar factories and strategies for better utilization of microbial benefits, aiming for sustainable improvements in sucrose extraction. However, extensive research is necessary to identify and characterize suitable bacterial species and how best to exploit them.