A micro-cavity in-line Mach-Zehnder interferometer (μIMZI) is an optical sensing structure fabricated in an optical fiber. Its design allows for refractive index sensing of liquid and gas in picoliter volumes, making it suitable for biochemical and medical sensing where measured material is often scarce. The fabricated structures show satisfactory levels of sensitivity, from about 400 nm/RIU in the near-water range of solutions (nD 1.336±0.003 RIU) to about 16 000 nm/RIU for solutions in approximate range from nD = 1.35 RIU to nD = 1.4 RIU. The structures were subjected to oxygen plasma, the process which was supposed to modify physical parameters of the structures, i.e., cavity surface wettability and roughness, and in consequence their sensitivity. As a result of the oxygen plasma modification we have observed a improved wettability of the structure surface, what makes it easier to introduce liquid into the cavity and simplifies the measurement process. In the case where the plasma processing is preceded by biological layer deposition, the bottom surface of the structure is smoothed and slightly deepened, causing a shift in the transmission spectrum and change in sensitivity.