In this paper, we propose a novel metamaterial-based microfluidic sensor that permits the monitoring of properties of the fluid flowing in the microfluidic reservoir embedded between the composite left–right handed (CLRH) microstrip line and the ground plane. The sensor’s working principle is based on the phase shift measurement of the two signals, the referent one that is guided through conventional microstrip line and measurement signal guided through the CLRH line. At the operating frequency of 1.275 GHz, the CLRH line supports electromagnetic waves with group and phase velocities that are antiparallel, and therefore the phase “advance” occurs in the case of CLRH line, while phase delay arises in the right-handed (RH) frequency band. The change of the fluid’s properties that flow in the microfluidic reservoir causes the change of effective permittivity of the microstrip substrate, and subsequently the phase velocity changes, as well as the phase shift. This effect was used in the design of the microfluidic sensor for the measurement of characteristics of the fluid that flows in the microfluidic reservoir placed under the CLRH line. The complete measurement system was developed including the Wilkinson power divider that splits the signal between conventional RH and CLRH section, transmission lines with the microfluidic reservoirs, and a detection circuit for phase shift measurement. Measurement results for different fluids confirm that the proposed sensor is characterized by relatively high sensitivity and good linearity (R2 = 0.94). In this study, the practical application of the proposed sensor is demonstrated for the biomass estimation inside the microfluidic bioreactors, which are used for the cultivation of MRC-5 fibroblasts.