The effective design of affinity ultrafiltration processes using a selective macroligand requires a detailed understanding of the effects of ligand-binding interactions on product yield and purification. Theoretical calculations were performed to evaluate the performance of affinity diafiltration separations with both competitive and independent binding interactions for the product and impurity. The intrinsic selectivity for independent binding decreased during the diafiltration due to the increase in fractional impurity binding as the impurity is selectively removed. The opposite behavior was seen for competitive binding because the strongly bound product displaces the impurity from the binding sites. Purification-yield diagrams were used to examine the effects of affinity-ligand concentration and binding constants on the separation. Model calculations were in excellent agreement with experimental data for the separation of tryptophan isomers using bovine serum albumin as the steroselective macroligand. Simulations with a fixed number of diavolumes show a clear optimum in product yield and purification factor at an intermediate ligand concentration due to the competing effects of the intrinsic selectivity and the rate of impurity removal. These results provide an appropriate framework for the design and optimization of affinity ultrafiltration systems.