The metabolic state of bacteria significantly contributes to their resistance to antibiotics; however, the specific metabolic mechanisms conferring antimicrobial resistance in
Helicobacter pylori
remain largely understudied. Employing transcriptomic and non-targeted metabolomics, we characterized the metabolic reprogramming of
H. pylori
when challenged with antibiotic agents. We observed a notable increase in both genetic and key proteomic components involved in fatty acid biosynthesis. Inhibition of this pathway significantly enhanced the antibiotic susceptibility of the sensitive and multidrug-resistant
H. pylori
strains while also disrupting their biofilm-forming capacities. Further analysis revealed that antibiotic treatment induced a stringent response, triggering the expression of the
hp0560-hp0557
operon regulated by Sigma28 (σ
28
). This activation in turn stimulated the fatty acid biosynthetic pathway, thereby enhancing the antibiotic tolerance of
H. pylori
. Our findings reveal a novel adaptive strategy employed by
H. pylori
to withstand antibiotic stress.