Bio-energy receives newfound attention in light of rising energy and operational costs in the context of operating Wastewater Treatment Plant. There is a way to explore the hidden potential of drawing a connection between bio-energy production and its subsequent reuse for on-site facilities. Two major researches have been investigated. The innovative bioreactors for pollution control and production of bio-energy and value added products from animal manure and fruit processing wastes was investigated for both laboratory and pilot plant studies. It was found that a significant amount of bio-gas was produced from the wastewater. This was due to the development of the bioreactor known as Bio-nest, which is able to provide a better sludge distribution, dead zone, and higher organic loading for the treatment of milk parlor wastewater with high lipid/fat content. Furthermore, an evaluation of bio-processed fruit waste into an added value by-product. Other parameters investigated include development of pre-treatment procedures, bio-process kinetics, and design/operation criteria. A relationship of required aeration time, pH, dissolved oxygen, and oxidation reduction potential curves during yeast growth was developed. The protein enhanced product from the bio-process fruit waste was subject to a shrimp feeding trial. It was found that it provided a similar cumulative mean growth as commercial feed and similar cumulative FCR (feed conversion ratio) as a controlled diet. This combined effort of treatment may provide an effective utilization of an existing wastewater treatment system as well as an affect on the food waste management system to achieve a sustainable environmental system.