The present paper reports a bacteria autonomous controlled concentrator prototype with a user-friendly interface for bench-top applications. It is based on a microfluidic lab-on-a-chip and its associated custom instrumentation, which consists of a dielectrophoretic actuator, to preconcentrate the sample, and an impedance analyzer, to measure concentrated bacteria levels. The system is composed of a single microfluidic chamber with interdigitated electrodes and an instrumentation with custom electronics. The prototype is supported by a real-time platform connected to a remote computer, which automatically controls the system and displays impedance data used to monitor the status of bacteria accumulation on-chip. The system automates the whole concentrating operation. Performance has been studied for controlled volumes of Escherichia coli samples injected into the microfluidic chip at constant flow rate of 10 L/min. A media conductivity correcting protocol has been developed, as the preliminary results showed distortion of the impedance analyzer measurement produced by bacterial media conductivity variations through time. With the correcting protocol, the measured impedance values were related to the quantity of bacteria concentrated with a correlation of 0.988 and a coefficient of variation of 3.1%. Feasibility of E. coli on-chip automated concentration, using the miniaturized system, has been demonstrated. Furthermore, the impedance monitoring protocol had been adjusted and optimized, to handle changes in the electrical properties of the bacteria media over time.