The coronavirus SARS-CoV-2 remains stable and highly infective in water for a long time, which makes the removal of virus from water an important approach to contain and block its spread. In this study, an antibody-engineered microrobot (AB-robot) was fabricated by using click chemistry to functionalize self-actuating Bacillus subtilis with neutralizing antibody P2C-1F11 against the SARS-CoV-2 S protein. The AB-robot can efficiently capture and remove SARS-CoV-2 from water by targeting SARS-CoV-2 S protein with P2C-1F11. The AB-robot displays rapid self-actuation capability in various aquatic media, including drinking water and tap water. And the virus clearance percentage of AB-robot in water was up to 95% against SARS-CoV-2 pseudovirus contaminant model. Moreover, scanning electron microscopy images show that a large number of virus particles were tethered to the surface of the AB-robot, further demonstrating the effective capture capability of the AB-robot. In summary, the significant contributions of both the P2C-1F11 for virus targeting and the fast microrobot motion for contacting the virus toward immediate capture and efficient removal of SARS-CoV-2 pseudovirus, which has potential application for preventing and blocking the spread of SARS-CoV-2 in water.