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Herein, T4‐bacteriophage‐funcionalizated magnetic Janus micromotors are used for the first time for highly selective Escherichia coli (E. coli) recognition and detection. The micromotors propel at speeds of up to 40 µm s−1 in complex biological samples for on‐the‐fly capture of E. coli "strain B"‐thiolated T4 bacteriophage complex. Detection is achieved by a simplified colorimetric readout in connection with gold nanoparticles. The detection limit meets the cut‐off for the fast diagnosis of urinary tract infections. The bacteriophage‐engineered micromotors are tested on bacteria isolated from urine samples and in serum isolated from negative blood cultures from hospital patients with excellent selectivity and reliability. The new strategy described here holds considerable promise for the multiplexed detection of a myriad of bacteria strains using tailored bacteriophages. Technically, this is the first microplate‐reader integrated micromotor approach, crossing another bridge from the research lab to the practical use of micromotors. Specifically, these results represent a qualitative step forward in the use of micromotor technology with sophisticated functionalization for fast bacteria screening in clinical settings. [ABSTRACT FROM AUTHOR]