Microfluidics-based separation of biomolecules has numerous applications, including fundamental characterization of biomolecules, sequencing of genomes for biological functions, biometric fingerprinting, and identification of pathogens and genetic diseases. One of the main drawbacks, however, for making microfluidic based separations more commercially viable is the non-specific adsorption of biomolecules at the channel walls during separations. Herein, we compare five commonly employed surface coatings, and evaluate their performance in terms of successful silanization of channel surface walls, long term stability, and antifouling performance, using BSA or IgG as model proteins. We compare adsorption of fluorescently-tagged proteins on glass slides with those confined within channels, showing similar behavior with static measurements, but differences when incorporating electrokinetic flow. Based on these data, we find that MPEG is an effective surface coating for applications where long term stability is critical. However, for separation experiments, where the channel is used shortly after coating, a silanized zwitterionic sultone has superior anti-fouling characteristics.