Methane (CH4) and ammonia (NH3) are emitted to the atmosphere during anaerobic processing of organic matter, and both gases have detrimental environmental effects. Methane conversion to biofuel production has been suggested to reduce CH4 emissions from animal manure processing systems. The purpose of this research is to evaluate the change in CH4 and NH3 emissions in an animal feeding operation due to biofuel production from the animal manure. Gas emissions were measured from swine farms differing only in their manure management treatment systems (conventional vs. biofuel). By removing organic matter (i.e., carbon) from the biofuel farms’ manure-processing lagoons, average annual CH4 emissions were decreased by 47% compared with the conventional farm. This represents a net 44% decrease in global warming potential (CO2 equivalent) by gases emitted from the biofuel farms compared with conventional farms. However, because of the reduction of methanogenesis and its reduced effect on the chemical conversion of ammonium (NH4 +) to dinitrogen (N2) gas, NH3 emissions in the biofuel farms increased by 46% over the conventional farms. These studies show that what is considered an environmentally friendly technology had mixed results and that all components of a system should be studied when making changes to existing systems.