Grafted semi-interpenetrating polymer networks (IPNs) were prepared from polyurethane (PU) prepolymers with polyester soft segments and hard segments containing carboxylic functional groups as well as polymethacrylate (PM) prepolymers with tertiary amine functional groups. The dependence of morphological and mechanical properties on the concentration of functional groups was studied. The enhanced miscibility of PU and PM prepolymers was observed at concentrations of functional groups of 0.25 mmol/g of polymer and above. Despite the improved miscibility, the PM prepolymers showed a tendency toward phase separation. Because the observed glass-transition temperature shifts of PU prepolymers indicated substantial miscibility, we ascribed this phenomenon to the presence of methyl methacrylate rich sequences in the PM prepolymer. The observed changes in mechanical properties by increasing the content of functional groups were typical for ionomers. Young's modulus increased as a result of physical interactions between functional groups. A significant drop in tensile strength was observed in IPN samples with phase-separated PU and PM prepolymers.