Transglutaminase 2 (TG2), mediating post‐translational modifications of multiple intracellular enzymes, is involved in the pathogenesis and progression of cancer. We used 1H‐NMR metabolomics to study the effects of AA9, a novel TG2 inhibitor, on two breast cancer cell lines with distinct phenotypes, MCF‐7 and MDA‐MB‐231. AA9 can promote apoptosis in both cell lines, but it is particularly effective in MD‐MB‐231, inhibiting transamidation reactions and decreasing cell migration and invasiveness. This metabolomics study provides evidence of a major effect of AA9 on MDA‐MB‐231 cells, impacting glutamate and aspartate metabolism, rather than on MCF‐7 cells, characterized by choline and O‐phosphocholine decrease. Interestingly, AA9 treatment induces myo‐inositol alteration in both cell lines, indicating action on phosphatidylinositol metabolism, likely modulated by the G‐protein activity of TG2 on phospholipase C. Considering the metabolic deregulations that characterize various breast cancer subtypes, the existence of a metabolic pathway affected by AA9 further points to TG2 as a promising hot spot. The metabolomics approach provides a powerful tool to monitor the effectiveness of inhibitors and to better understand the role of TG2 in cancer.