Abstract Background & Aims The mechanism of action of anti-TNF agents could implicate macrophages modulation in Crohn’s disease (CD). As CD macrophages are defective to control CD-associated adherent-invasive E. coli (AIEC), anti-TNF agents could limit AIEC replication within macrophages. We assessed the effect of anti-TNF agents on AIEC survival within monocytes-derived macrophages (MDM) from CD patients and attempted to identify the implicated proteins. Methods Peripheral blood monocyte-derived macrophages (MDM) were obtained from 44 CD patients including 22 with and 22 without anti-TNF agents. MDM were infected with AIEC-LF82 reference strain. Proteomic analysis was performed before and 6h after AIEC-LF82 infection. Results AIEC-LF82 survival was lower in MDM from CD patients receiving anti-TNF agents compared to those who did not (-73%, p=0.006). After AIEC-LF82 infection, the levels of CD82 (p=0.007), ILF3 (Interleukin enhancer-binding factor 3; p=0.001), FLOT-1 (Flotillin-1; p=0.007) and CHI3L1 (Chitinase 3-like 1; p=0.035) proteins were different within CD-MDM depending on anti-TNF exposure. FLOT-1 (ϱ=- 0.44; p=0.038) and CHI3L1 (ϱ=0.57, p=0.006) levels were inversely and positively correlated with AIEC survival within MDM from CD patients with or without anti-TNF, respectively. We observed a dose-dependent decrease of AIEC-LF82 survival after adjunction of anti-TNF within MDM inducing increase of FLOT-1 and decrease of CHI3L1 mRNA levels. Neutralization of intra-macrophagic CHI3L1 protein using anti-CHI3L1 antibodies reduced AIEC survival within macrophages 6h after infection (p<0.05). Conclusion Anti-TNF agents are able to restrict replication of pathobiont, such as AIEC, within macrophages by modulating FLOT-1 and CHI3L1 expressions in CD patients.