Conjugated linoleic acid (CLA) is an unsaturated fatty acid with many active functions. Here, we demonstrate quorum sensing (QS) to study mechanisms involved in CLA production of L. fermentum L1. Addition of linoleic acid (LA) with increased concentration results in promising CLA production of 2.22–10.36 mg/mL, cell density and autoinducer-2 (AI-2) involved in QS of L1. Further, proteomics analysis quantified up-expression of 185 differentially expressed proteins (DEPs) upon addition substrate of 8% LA, including myosin cross-reactive antigen protein, enolase (eno), and S-ribosylhomocysteine lyase (luxS), while 174 DEPs were down-regulated. Furthermore, S-Adenosyl-l-methionine metabolic pathway involved in luxS/AI-2 QS system was up-regulated. Additionally, protein-protein interaction network leverage key proteins, luxS and eno responsible for CLA production. Finally, furanone inhibitor block luxS/AI-2 QS system to allow AI-2 content, CLA, and cell density of L1 to decrease level. Western blot analysis confirmed, furanone successfully inhibited expression of luxS and eno. Whereas, luxS/AI-2 QS system was activated with LA results in increase expression of eno and production of CLA. Collectively, this study provides a new mechanism of CLA production by lactic acid bacteria.