Ionic liquids provide challenges and opportunities for sustainable industrial developments. However, the toxic impacts of ionic liquids reported by many researchers cannot be overlooked. Therefore, in this chapter, we introduce the antimicrobial activities of ionic liquids in bioprocesses and, in greater detail, we discuss their environmental impacts, including the toxicity, biodegradability, bioaccumulation, and mobility of ionic liquids. We believe that this presented information will support colleagues engaged in ionic liquid-related fields. Graphical Abstract.