Poly(methyl methacrylate) (PMMA) flow-cells containing microwells were deposited with different nonspecific binding blocking agents namely bovine serum albumin (BSA), cationic lipid (DOTAP) and diethylene glycol dimethyl ether (DEGDME). Water contact angle (WCA) and atomic force microscope (AFM) measurements were carried out to confirm the successful depositions of BSA, DOTAP, DEGDME onto the PMMA surfaces. Fluorescent intensity measurements were performed to evaluate the degree of non-specific adsorption of Cy5-labeled anti-IgG proteins onto plain and oxygen plasma treated (PT) PMMA flow-cells as well as PMMA flow-cells deposited with different above-mentioned blocking agents. We then employed a label-free detection method called total internal reflection ellipsometry (TIRE) to evaluate the stability of the deposited blocking agents inside the PMMA flow-cells. It was found that while DOTAP was the best agent for blocking the non-specific adsorption, it could be removed from the PMMA surfaces of the flow-cells upon rinsing with phosphate buffer saline (PBS) and later deposited back onto the Au-coated glass sensing substrate of the TIRE. The removal of the blocking agents from PMMA surfaces and their deposition onto the sensing substrate were further manifested by measuring the kinetics and the amount of adsorbed anti-a-hCG proteins. Overall, the dry DEGDME coating by plasma enhanced chemical vapor deposition (PECVD) showed very good blocking and excellent stability for subsequent assay inside the microwells. Our results could be useful when one considers what blocking agents should be used for PMMA-based microfluidic immunosensor or biosensor devices by looking at both the blocking efficiency and the stability of the blocking agent.