An entirely water-based, energy self-sufficient, integrated in-line waste management system is provided for comprehensive conversion of all organic fractions of municipal and wider community waste to fuels suitable for use in transportation, with all solid residues converted to high nutrition compost. The system is based on a combination of pre-treatment, involving alkaline hydrolysis and saponification; three-way separation of the pre-treated waste into different streams that are each directed to suitable further processing including fuel production; which includes biodiesel generation in a continuous-flow catalytic esterification unit, and anaerobic digestion to produce methane or other small molecule biofuel. Remaining solids are converted to compost in a quasi-continuous process.