Microfluidic design has advanced existing protein separation capabilities and supported novel assays. Key metrics for successful protein separations include fast, robust, and sensitive analysis of complex mixtures of bio-macromolecules. Attaining high separation resolution is a chief concern. Here we review recent advances in polymer-based electrophoresis sieving materials that are impacting microfluidic bioanalytical applications. Looking forward, we comment on unmet needs for advanced separation media in micro-to-nanoscale devices.