The dairy industry is showing renewed interest in anaerobic digestion in response to environmental regulations and the need to control odor. To plan effectively, nutrient management planners need to know how manure is transformed during anaerobic digestion. Anaerobic digestion alone does not result in a large decrease in mass (approximately 5% reduction). Thus it is crucial to confirm that a farm has adequate cropland for spreading manure before investing in an anaerobic digester, including calculation of the appropriate phosphorus index and a whole-farm P mass balance (including food waste P if indicated in the plan). (If cropland is not adequate, then a plan for exporting nutrients off-farm may be necessary.) The total amounts of N and P remained about the same in samples taken monthly from the influent and effluent of three digesters over a two-year period; however, there was a shift from organic forms to inorganic forms. Ammonia increased by 37% and ortho-P increased by 26%. Thus anaerobic digestion increased the plant availability of N and P, but also increased the susceptibility to loss by leaching and volatilization. Digested manure is typically separated into solid and liquid streams, with variable nutrient partitioning. It is important to get site-specific samples for nutrient analysis from these waste streams prior to application to cropland, especially the liquid stream, which may undergo further transformations during storage. When applying digested manure to cropland for corn production, the higher levels of ammonia increase the importance of rapid incorporation to minimize volatile losses of N. The reduced odor of digested manure allows it to be spread on hay in the summer when the potential for complaints about odor is greatest, and the potential for runoff and leaching are less, due to drier soil conditions and more immediate crop uptake.