Quinolones of the human pathogen Pseudomonas aeruginosa serve as antibacterial weapons and quorum sensing signals and coordinate the production of important virulence factors. A central enzyme for the biosynthesis of these quinolones is the synthetase PqsD. We developed an activity-based probe strategy that allows to screen for PqsD inhibitors in a cellular model system of live cells of Escherichia coli overexpressing PqsD. This strategy allowed us to determine IC50 values for PqsD inhibition directly in live cells. Our most potent inhibitors were derived from the anthranilic acid core of the native substrate and resulted in single-digit micromolar IC50 values. The effectiveness of our approach was ultimately demonstrated in P. aeruginosa by the complete shutdown of the production of quinolone quorum sensing signals and quinolone N-oxides and a considerable inhibition of the production of phenazine virulence factors.