Polymer mixtures based on native corn flour and synthetic biodegradable polyester are prepared in one processing step. Melt mixing is performed in a laboratory micro‐compounder. Starch contained in native corn flour is plasticized either by commonly used glycerol/water mixture or by two types of ionic liquids, 1‐allyl‐3‐methylimidazolium chloride, and 1‐butyl‐3‐methylimidazolium chloride. Efficiency of plasticizers on the compatibility of native corn flour with polyester and starch plasticizing ability is evaluated and compared. The structure of mixtures is examined using scanning electron microscopy and wide‐angle X‐ray scattering. It is found that the plasticizer applied has a crucial effect on the resulting morphology. Both ionic liquids show a better plasticizing effect on starch compared to the traditional glycerol/water plasticizer.