Biological treatment pond system has been adopted by Malaysian palm oil mills to treat palm oil mill effluent (POME). Conventional treatment pond system is no longer able to comply with the new legislation requirements as implemented and enforced by Department of Environment (DOE) recently. Various tertiary POME treatment technologies have been introduced, they are not without disadvantages such as sludge generation. Revolutionary Organic Onsite Treatment System (ROOTS) is a microbial enzyme system specially formulated for organic based effluent treatment. ROOTS was installed in Johor after the palm oil mill existing anaerobic ponding system with capacity 40 MT hr^-1. The mill is having four facultative ponds 1, 2, 3 and 4 respectively. The enzyme dosing system was installed at facultative pond 1. Predetermined numbers of maintenance-free diffusers and biomedia were mounted at facultative ponds 1, 2 and 3. The system configuration is originally applied for food industries waste water. Results from a year observation showed that the final POME discharge complied with DOE Standard A discharge limit (Johor State).