Exposure to live bacteria and accumulation of dead bacteria during bactericidal processes can cause bacterial infectious diseases, implant failure, and antibacterial surface deterioration. Microcapsules with asymmetrically distributed, funnel-shaped pores, which are capable of capturing, retaining, and killing bacteria are developed, offering a solution to bacterial contamination in liquids. It is found that bacterial isolation inside microcapsules is mainly driven by the bacteria's own motility and the microcapsules' geometry. After entry into the microcapsule cavity, the bacteria are stably retained inside. The microcapsules shield surrounding cells from exposure to bacterial toxins, as demonstrated by the coculture of rat embryonic fibroblast cells with microcapsules loaded with live Escherichia coli. The microcapsules can be enhanced with a bactericidal coating covering only the interior cavity. This confines the bacteria-killing process, thereby further increasing biocompatibility. The microcapsules may offer a viable bacteria combatant approach as a potentially advantageous method to eradicate bacterial contamination.