Clearance of bacteria-secreted toxins can be a benefit to treating bacterial infections. In this study, we show a polydiacetylene (PDA) nanoparticle-functionalized microgel for managing topical bacterial infections. These functional microgels with designed shapes and size are precisely fabricated via a digital light processing (DLP)-based 3D bioprinting process. The PDA nanoparticles that can bind and neutralize pore-forming toxins (PFTs) are installed in the microgels by readily mixing within the monomer solution followed by 3D printing. PFTs can diffuse into the microgels and subsequently are captured and neutralized by the PDA nanoparticles. In the mouse model, the local injection of the microgels promotes tissue recovery after bacterial infections. This work presents a PDA nanoparticle-functionalized microgel for topical bacterial infection treatments by removing PFTs, which could inspire future infection treatments.