Synchrotron SAXS was used to characterize the morphology of an amorphous ionomer-compatibilized polyester/polyamide blend. This technique was shown to provide very useful information regarding the size of the dispersed domains, the structure of the phase-separated morphology, and the thickness of the blend interface. Two blend series that were investigated include a binary system (polyamide/ionomer) with varying ion contents of the polyester ionomer and a ternary blend (polyamide/polyester/ionomer) with increased loading of an ionomer compatibilizer. The incorporation of ionic functionality, by varying either ion content or ionomer loading, has a significant impact on the sizes of the dispersed domains with both blend systems showing a trend toward smaller domain sizes with an increase in the concentration of ionic functionality. In addition, the 50/50 blend series indicates that the ionic incorporation also leads to a shift in the morphology to a more elongated, cocontinuous structure. While the ionic functionality does affect the domain sizes and structure, the location of the functional groups at the blend interface does not lead to an increase in the thickness or diffusivity of the interfacial region.