Membrane-based microfiltration is a gold standard widely used in clinical applications, water treatment, or water safety monitoring for sample processing to purify or concentrate targeted microparticles in a sample liquid. In the concentration of targeted microparticles, membrane fouling is one of the main problems contributing to a low recovery rate. Research efforts to improve the recovery rate focus on membrane materials, chemical treatment, or physical techniques. Periodic backwashing and acoustic vibration are the most used physical techniques to release clogged microparticles on the membrane surface. However, they are less effective for low concentrations of microparticles. In addition, highintensity acoustic vibration and high-pressure backwashing are incompatible with bioparticle processing, such as Escherichia coli (E. coli) bacteria. Herein, we proposed a Dean vortex-assisted cross-flow microfilter with a spiral-shaped microchannel to improve the recovery rate of the E. coli concentration in water samples. The Dean vortex formed in the microchannel efficiently prevented the clogging of E. coli on the membrane surface, demonstrating a significantly improved recovery rate from ∼40 to >90%. Moreover, we applied the Dean vortex-assisted cross-flow microfilter for concentrating E. coli spiked in tap water samples, proving its potential for real-life applications in processing low-concentration bacterial samples in environmental and water safety monitoring.