In this paper, we propose a novel microwave microfluidic sensor with dual-sensing capability. The sensor is based on a dual-mode resonator that consists of a folded microstrip line loaded with interdigital lines and a stub at the plane of symmetry. Due to the specific configuration, the resonator exhibits two entirely independent resonant modes, which allows simultaneous sensing of two fluids using a resonance shift method. The sensor is designed in a multilayer configuration with the proposed resonator and two separated microfluidic channels—one intertwined with the interdigital lines and the other positioned below the stub. The circuit has been fabricated using low-temperature co-fired ceramics technology and its performance was verified through the measurement of its responses for different fluids in the microfluidic channels. The results confirm the dual-sensing capability with zero mutual influence as well as good overall performance. Besides an excellent potential for dual-sensing applications, the proposed sensor is a good candidate for application in mixing fluids and cell counting.