Pseudomonas aeruginosa has emerged as a serious nosocomial threat with a high morbidity and mortality rate, especially in immunocompromised patients. Its pathogenicity is attributed to the virulence modulating -quorum sensing system. The coexistence of Chlorella emersonii KJ725233, a novel microalga with P. aeruginosa, pointed to its subterfuge to alter the pathogenicity of its partners. The study was, thus, aimed at determining the ability of CEK to modulate the pathogenesis of the aggressor P. aeruginosa. With a MIC of 0.5 mg mL −1 , the methanolic extract of C. emersonii KJ725233 was able to inhibit the synthesis of pyocyanin (62.48 ± 1.11%), protease (84.72 ± 1.11%), elastase (73.47 ± 0.11%), pyochelin (69.95 ± 7.12%), rhamnolipid (86.76 ± 0.48%), and polysaccharide (44.72 ± 1.58%) which are established virulence factors of P. aeruginosa. RT-PCR studies indicated the downregulation of its quorum sensing genes, lasI (84.63 ± 5.98%), lasR (85.56 ± 3.45%), rhlI (88.33 ± 3.56%), rhlR (88.73 ± 2.91%), and pqsA (72.61 ± 1.91%) which are known to play a crucial role in the pathogenesis of the organism. The presence of phytol in the methanolic extracts was indicated by its GC-HRMS analysis. With an ability to effectively incapacitate the virulence system of P. aeruginosa, C. emersonii KJ725233 presents itself as an efficient disarming agent with a potential use in pharmaceutical formulations.