Proteases play a role in different processes for protozoans and for the free-living amoeba Acanthamoeba. Some of these processes are related to pathogenicity and to encystment. In this study we describe the discovery of a protease with antimicrobial activity produced by Acanthamoeba. To identify it, we developed a novel zymogram using bacteria as an in-gel substrate that can help identify proteins capable of bacterial degradation. We used chromatography to isolate the proteases and showed that it quickly degrades in the environment. Additionally, we identified overexpressed proteases during encystment. The study of proteases from Acanthamoeba can serve several purposes including new antimicrobial proteins that the amoeba can use for potentially predigesting prokaryotes. Secondly, it can help with the identification of potential new therapies against Acanthamoeba infection.