Molecularly imprinted polymers (MIPs) emerged half a century ago have now attracted tremendous attention as artificial receptors or plastic antibodies. Although the preparation of MIPs targeting small molecules, peptides, or even proteins is straightforward and well-developed, the molecular imprinting of microorganisms still remains a big challenge. This review highlights the preparation of MIPs that reveal biomimetic specificity and selectivity towards microorganisms by creating the well-defined cell recognition sites. We present the state-of-the-art strategies for the expeditious synthesis of MIPs targeting microorganism including surface components imprinting, cell mediated lithography, and microcontact stamping. These receptor-like biomimetic materials have garnered increasing attention in different fields. In this review, we also describe the diverse applications of microorganism-imprinted polymers such as microbial activation, microbial fuel cells, and microorganism detection and sensing. The major challenges and further prospects on the design of microorganism-imprinted polymers is also outlined.