The ability of antimicrobial peptides (AMPs) for effective binding to multiple target microbes has drawn lots of attention as an alternative to antibodies for detecting whole bacteria. We investigated pathogenic Escherichia coli (E. coli) detection by applying a microfluidic based biosensing device embedded with AMP-labeled beads. According to a new channel design, our device is reusable by the repeated operation of detection and regeneration modes, and the binding rate is more enhanced due to even distribution of the bacterial suspension inside the chamber by implementing influx side channels. We observed higher binding affinity of pathogenic E. coli O157:H7 for AMP-labeled beads than nonpathogenic E. coli DH5α, and the fluorescence intensity of pathogenic E. coli was about 3.4 times higher than the nonpathogenic one. The flow rate of bacterial suspension should be applied above a certain level for stronger binding and rapid detection by attaining a saturation level of detection within a short time of less than 20 min. A possible improvement in the limit of detection in the level of 10 cells per mL for E. coli O157:H7 implies that the AMP-labeled beads have high potential for the sensitive detection of pathogenic E. coli at an appropriate flow rate.