One of the major issues in microfluidic biosensors is biolayer deposition. Typical manufacturing processes, such as firing of ceramics and anodic bonding of silicon and glass, involve exposure to high temperatures, which any biomaterial is very vulnerable to. Therefore, current methods are based on deposition from liquid, for example, chemical bath deposition (CBD) and electrodeposition (ED). However, such approaches are not suitable for many biomaterials. This problem was partially resolved by introduction of ceramic–polymer bonding using plasma treatment. This method introduces an approximately 15-min-long window for biomodification between plasma activation and sealing the system with a polymer cap. Unfortunately, some biochemical processes are rather slow, and this time is not sufficient for the proper attachment of a biomaterial to the surface. Therefore, a novel method, based on plasma activation after biomodification, is introduced. Crucially, the discharge occurs selectively; otherwise, it would etch the biomaterial. Difficulties in manufacturing ceramic biosensors could be overcome by selective surface modification using plasma treatment and bonding to polymer. The area of plasma modification was investigated through contact-angle measurements and Fourier-transform infrared (FTIR) analyses. A sample structure was manufactured in order to prove the concept. The results show that the method is viable.