An advanced methane and ammonia recovery system captures gaseous waste produced by domestic livestock to reduce the release of greenhouse gasses into the atmosphere and to generate energy. The system includes a gas capture system residing at a peak of a barn. At large commercial operations, the captured gasses pass through a separator to separate methane from ammonia gas. The ammonia is processed to obtain a fertilizer. The methane is stored in a tank, and drawn from the tank to provide fuel for an electrical generator. At smaller operations, the captured gasses may be stored in a tank for periodic collection by a tanker truck or other transportation, or where economically feasible, piped to a central processing location. The system is designed to substantially reduce the amount of methane gas released into the environment while providing additional income to the domestic livestock operations.