Study shows that stem rot of coffee at the University of Southern Mindanao is caused by Sclerotium rolfsii. Pathogenicity test revealed that the fungus was pathogenic to stem cutting of coffee. First noticeable symptom of infection was girdling at the base of the stem where it was in contact with the soil which eventually encircled the plant stem at 5 days after inoculation. Application of Organic Based Control Agents (OBCAs) either as protectants or eradicants reduced percentage severity infection and controlled stem rot of coffee. These OBCAs are potential alternatives to manage stem rot of coffee, and can be used as substitute to synthetic pesticides. These are organic-based hence, safe and environment-friendly.