Alternative methods for applying livestock manure to no-till soils involve environmental and economic trade-offs. A process-level farm simulation model (Integrated Farm System Model) was used to evaluate methods for applying liquid dairy (Bos taurus L.) and swine (Sus scrofa L.) manure, including no application, broadcast spreading with and without incorporation by tillage, band application with soil aeration, and shallow disk injection. The model predicted ammonia emissions, nitrate leaching, and phosphorus (P) runoff losses similar to those measured over 4 yr of field trials. Each application method was simulated over 25 yr of weather on three Pennsylvania farms. On a swine and cow-calf beef operation under grass production, shallow disk injection increased profit by $340 yr(-1) while reducing ammonia nitrogen and soluble P losses by 48 and 70%, respectively. On a corn (Zea mays L.)-and-grass-based grazing dairy farm, shallow disk injection reduced ammonia loss by 21% and soluble P loss by 76% with little impact on farm profit. Incorporation by tillage and band application with aeration provided less environmental benefit with a net decrease in farm profit. On a large corn-and-alfalfa (Medicago sativa L.)-based dairy farm where manure nutrients were available in excess of crop needs, incorporation methods were not economically beneficial, but they provided environmental benefits with relatively low annual net costs ($13 to $18 cow). In all farming systems, shallow disk injection provided the greatest environmental benefit at the least cost or greatest profit for the producer. With these results, producers are better informed when selecting manure application equipment.