This paper describes the synthesis and unique functionalities of protein microtube motors with an exterior surface consisting of avidin (Avi). Using wet-template synthesis with layer-by-layer (LbL) assembly in a track-etched polycarbonate (PC) membrane, we fabricated precursor microtubes having an internal wall composed of Pt nanoparticles (PtNPs). Subsequently, hollow cylinders eliminated from the PC template were dispersed in water and were wrapped electrostatically with Avi by LbL coating. The obtained tubules (1.2 μm outer diameter, 24 μm length) are catalytically self-propelled in aqueous H2O2 solution by jetting O2 bubbles from the open-end terminus. Avidin–biotin complexation allows the swimming microtubes to capture various biotinylated substances. The fluorescent biotin was bound selectively to the tube outer surface, even with the coexistence of other dyes. Biotin-labeled nanoparticles and microparticles were adsorbed tightly and were transported without being shaken off. Furthermore, the self-stirring motion of biotinylated-α-glucosidase-covered microtubes accelerated the enzyme reaction. It is noteworthy that the protease digested the multilayered cylindrical walls. These results demonstrated that the swimming protein microtubes act as ultrasmall transporters, separator, and stirrers with a good biofriendly nature.