Two common manure storage practices are stockpiles and lagoons. The manure from stockpiles is applied to soils in solid form, while lagoon manure is applied as a liquid. Soil amendment with manure in any form introduces a significant amount of phosphorus (P) that exists in both organic and inorganic forms. However, little is known about P speciation in manure stored under different conditions, or the subsequent forms when applied to soils. We used solution (31)P nuclear magnetic resonance (NMR) spectroscopy and conventional P fractionation and speciation methods to investigate P forms in dairy manure and liquid lagoon manure, and to study how long-term amendment with these manures influenced surface and subsurface soil P speciation. Our results show that the P forms in solid and lagoon manure are similar. About 30% of the total P was organic, mostly as orthophosphate monoesters. On a dry weight basis, total P was much higher in the solid manure. In the manure-amended soils the total P concentrations of the surface soils were similar, regardless of manure type. Total P in the subsurface soil was greater in the lagoon-manure-amended soil than the solid-manure-amended subsurface soil. However, the fraction of organic P was greater in the subsurface of the solid-manure-amended soil. The NMR results indicate that the majority of organic P in the soils is phytic acid, which is enriched in the surface soils compared with the subsurface soils. These results provide insight into P speciation and dynamics in manure-amended soils that will further increase our understanding on how best to manage manure disposal on soils.