The present invention discloses a biological wastewater treatment system and its mode of operation that enables onsite treatment of organic wastewater, and simultaneous recovery of resources like bioenergy, reuse quality water, and organic manure. The treatment system uses microbial strains that are hydrolytic bacteria and methanogenic Archaea along with anaerobic protozoa and micro-metazoa. In comparison with the existing onsite wastewater treatment systems, the present invention has many advantages as it has immense application for small establishments like restaurants, catering units, canteens, small communities, houseboats, agro-based MSMEs, etc. and hence this will be a better substitute that will find wide application in many sectors.