Low molecular weight organic acids such as acetic acid, propionic acid and butyric acids generated from partial anaerobic treatment of palm oil mill effluent (POME) were recovered using pilot scale filtration and evaporation system. Mechanical filter press (14 L) was used for removing solid fractions and fraction distillation unit (40 L) for evaporation and clarification of concentrated acid from POME. Clarification using rotary evaporator was found to be more suitable than distillation column. Due to the presence of more than 90% of water in POME, the final clarified product comprises only 7% of the total volume. The material balance for the overall process was estimated and integrated system for the bioconversion of organic acids into polyhydroxyalkanoates (PHA) was proposed. The recovery of organic acids has a significant and economical impact, since around 50% cost of PHA production is believed to be associated with the substrate itself