Microbial signals trigger the release of neutrophil extracellular traps (NETs) through peptidyl-arginine-deiminase-4 (PADI4). In turn, NETosis can propagate inflammation to distant tissues. We hypothesize that PADI4 mediates the interactions between diet-modified microbiota and host metabolism. We report that in the adipose tissue of individuals with obesity, NETosis was associated with dysglycemia. In mice, high-fat diet (HFD) induced not only dysmetabolism and meta-inflammation but also local and systemic signs of NETosis. Deleting Padi4 in hematopoietic cells (Padi4KO) blunted liver and adipose inflammation and improved metabolism under HFD. While NETs were able to disrupt gut epithelial integrity, abrogating NETosis preserved intestinal barrier function and mitigated metabolic endotoxemia due to HFD. Padi4 deletion did not prevent diet-induced dysbiosis, but Padi4KO mice were protected from intestinal hyper-permeability and metabolic impairment due to the transfer of HFD-modified microbiota. As Padi4KO did not blunt the dysmetabolic effects of LPS, we conclude that NETosis operates at the microbiota-intestinal interface, inducing hyperpermeability and the systemic spillover of bacterial-derived products, paving the way to the metabolic consequences of HFD. Finally, pharmacologic PADI4 inhibition recapitulated findings obtained in Padi4KO mice on metabolism and liver steatosis, thereby uncovering a druggable role for PADI4 in mediating the metabolic effects of unhealthy microbiota.