This paper analyses energy flows on a dairy farm in Central Pennsylvania, U.S.A. Energy values for all inputs to the agricultural system are calculated and evaluated with respect to alfalfa, corn and milk production. An evaluation of nitrogen and phosphorus flows demonstrates the impact that the use of inorganic fertilizers has on the total energy budget of the farm system. The recycling of nutrients via the application of animal manures provides both a source of fertilizer and significant energy savings in terms of the energy costs necessary to produce a similar quantity of inorganic nutrients. Energy efficiencies appeared to be higher than for previous studies reported in the literature. Energy input—output analysis is introduced as an effective technique for tracing both direct and indirect energy flows within an agricultural system. The interdependency of alfalfa, corn, milk production and the management of animal manures is demonstrated with this analysis and the required inputs of fuels and electricity, goods, and solar energy inputs are calculated.