S. pneumoniae is widely recognized as a leading cause of respiratory infections worldwide, often resulting in high mortality rates. However, the advent of microfluidic technologies has brought significant advancements, including the simplified, sensitive, cost-effective, and rapid approach to pneumococcal bacteremia detection. In this study, we have revised the microfluidic magnetic platform patented by our research group to isolate the bacteria using synthesized micro-magnetic beads bonded with aptamer. In the initial phase of the experiments, the inlet flow rate was adjusted to match the rotational speed of the magnetic unit to retain the micro-magnetic beads within the fabricated microfluidic channel effectively. Subsequently, a series of experiments were conducted to assess microfluidics-based bacteria isolation at various flow rates, involving seven different concentrations of bacteria, and the outcomes were compared with those obtained through batch-type isolation method. The isolation selectivity of target bacteria from complex samples was also assessed with control bacteria at two different concentrations. Furthermore, the isolated micro-magnetic beads-bacteria complexes were also transferred to interdigitated microelectrodes unit for electro-chemical impedance spectroscopy analysis. The ultimate objective is to integrate the isolation and detection components on the same microfluidic platform which leads to a rapid and precise diagnosis of bacterial infections.