An alternating anaerobic and aerobic digestion system and method of forming same includes a subterranean enclosure configured to hold organic matter. The enclosure has a plurality of conduits in a bottom surface of the enclosure. The digestion system further includes an irrigation system configured to dispense a liquid from a top portion of the enclosure and to recover a percolated liquid from a bottom portion of the enclosure, a ventilation system configured to provide air flow to the bottom portion of the enclosure, and a gas-tight membrane cover configured to cover the enclosure.