This study aimed to identify and characterize lactic acid bacteria strains with antimicrobial activity against Proteus mirabilis, a gram-negative bacterium associated with Parkinson’s disease, Crohn’s disease, and nosocomial infections. Among the 987 lactic acid bacteria strains isolated from various sources, strain no. CHK903 showed high antimicrobial activity against P. mirabilis. Phylogenetic tree analysis based on the 16S rRNA gene and scanning electron microscope analysis identified the selected strain as the rod-shaped Weissella cibaria. The culture supernatants of W. cibaria CHK903 showed antimicrobial activity against some pathogens. Two antimicrobial compounds with molecular weights 189 and 365 Da were partially purified from the culture supernatants of W. cibaria CHK903 using Biogel P2 gel permeation column chromatography. The culture supernatants of W. cibaria CHK903 also showed significant antibiofilm properties, inhibiting biofilm formation by 90% and removing pre-formed biofilms by 60%. These findings suggest the potential therapeutic use of W. cibaria CHK903 as a natural antimicrobial against P. mirabilis-related infections.