Phosphatase and tensin homolog (PTEN) is a negative regulator for PI3K signaling essential for B cell development. To explore the physiological effects of PTEN mutation on peripheral B cells, we generated CD23/cre-PTEN Flox/Flox (CD23-cKO) mice in this study to avoid the developmental arrest. The mutant mice develop systemic inflammation associated with B cell expansion in the early phase followed with a severe immune cell-infiltration in multiple vital organs. PTEN deficiency leads to an accumulation of PI(3)P, an increase of lysosomal recruitment of TLR9/p38 complex, and an aberrant activation of TLR9/IL-6 axis in B cells. Interestingly, cholesterol biosynthesis pathway is upregulated in mutant cells upon TLR9 engagement. A blockade of cholesterol biosynthesis by targeting SQLE greatly reduces the level of PI(3)P and the interaction between TLR9 and p38, which lowers the level of TLR9-induced IL-6. Thus, PTEN represents a critical metabolic checkpoint that fine-tunes lipid and cholesterol homeostasis to control TLR9-driven inflammation.