Palm oil mill effluent (POME) is a by-product of the palm industry and it releases large amounts of greenhouse gases (GHGs). Water systems are also contaminated by POME if it is released into nonstandard ponds or rivers where it endangers the lives of fish and water fowl. In this paper, the environmental bottlenecks faced by palm oil production were investigated by analyzing the data collected from wet extraction palm oil mills (POMs) located in Malaysia. Strategies for reducing pollution and technologies for GHG reduction from the wet extraction POMs were also proposed. Average GHG emissions produced from processing 1 ton of crude palm oil (CPO) was 1100 kg CO2eq. This amount can be reduced to 200 kg CO2eq by capturing biogases. The amount of GHG emissions from open ponds could be decreased from 225 to 25 kg CO2eq/MT CPO by covering the ponds. Installation of biogas capturing system can decrease the average of chemical oxygen demand (COD) to about 17,100 mg/L and stabilizing ponds in the final step could decrease COD to 5220 mg/L. Using a biogas capturing system allows for the reduction of COD by 80% and simultaneously using a biogas capturing system and by stabilizing ponds can mitigate COD by 96%. Other ways to reduce the pollution caused by POME, including the installation of wet scrubber vessels and increasing the performance of biogas recovery and biogas upgrading systems, are studied in this paper.