Bacterial biofilms are composed of a consortium of bacteria that communicate with each other through quorum sensing. Therefore, bacteria can form an extracellular matrix, which is a mucus composed of exopolysaccharides, peptidoglycans, and extracellular DNA, through these communication molecules. The matrix protects the community of bacteria from the adverse effects of the external environment, including antibiotics, biocides, and eradicating agents. Self‐propelled functional microrobots offer great promises in the biomedical field. The self‐propelled microrobots represent an innovative platform in microrobotic research, aiming to have an important role in the biomedical field. One of the potential applications is removal of bacterial biofilms. Herein, the specific design of multifunctional microrobots is demonstrated using antimicrobial‐designed peptides for eradication of methicillin‐resistant Staphylococcus aureus (MRSA)‐produced biofilms. The designed microrobots can perform various tasks, including autonomous navigation toward bacterial cells, mechanical entry into bacterial biofilms, and blockage of the replication of bacterial DNA by indolicidin peptides. The implemented design extends the microrobot applications not only to the removal of biological aggregates but also to the delivery and release of drugs or even target manipulation, demonstrating their great potential for use in biomedical research.