Field trials in four distinct agricultural soils were conducted to examine changes to total recoverable and labile soil Cd and Ni concentrations with applications of commercial phosphate fertilizers. The edible portion of wheat and potato crops grown at the field plots were analyzed for recoverable Cd and Ni. Total recoverable Ni and Cd concentrations in agricultural soils increased by 10 and 22%, respectively, each year of the study at recommended application rates. Labile Cd and Ni were measured using diffusive gradients in thin films (DGT), a passive sampling device reported to estimate the plant bioavailable metal fraction. Nickel concentrations measured with DGT did not significantly change with treatment nor did they change over time. Cadmium concentrations measured with DGT increased with application rate and over time from 2003 to 2005, then decreased in 2006. Wheat grain Cd concentrations and Cd and Ni levels in tubers increased significantly with fertilizer treatment level. Grain and tuber Cd values exceeded the minimal risk levels for chronic oral exposure. At agronomical P-fertilizer application rates, 25% of plant samples deviated from the Cd minimal risk levels. The present study reports the use of Kd-BIO, defined as the ratio of total recoverable metal to DGT measured metal, as a significant indicator of crop metal accumulation in the edible portion. The Kd-BIO values were well correlated with both grain and tuber concentrations over multiple growing seasons. Results from long-term field trials emphasize Kd-BIO as a dynamic term that provides risk characterization information about the fate of Cd and Ni in aged, fertilized agricultural soils and crops.