Impedance spectroscopy is a common approach in assessing passive electrical properties of biological matter. However, several problems appear in microfluidic devices in connection with the requirement for high sensitivity of signal acquisition from small volume sensors. The developed compact and inexpensive analyzer provides impedance spectroscopy measurement from three sensors, both connected in direct and differential modes. Measurement deficiencies are reduced with a novel design of sensors, measurement method, optimized electronics, signal processing, and mechanical design of the analyzer. Proposed solutions are targeted to the creation of reliable point-of-care (POC) diagnostic and monitoring appliances, including lab-on-a-chip type devices in the next steps of development. The test results show the good working ability of the developed analyzer; however, also limitations and problems that require attention and further improvement are appointed.