Clitoria ternateaflowers are rich in anthocyanins and possess various biological activities. Specifically, the antibacterial mechanism of action ofC. ternateaanthocyanins remains unknown and was investigated inEscherichia coli. A time–kill assay was used to assess the antibacterial activity and the metabolic perturbations inE. coliwere investigated utilizing liquid chromatography–mass spectrometry (LC-MS)-based metabolomics. Pathway analyses were carried out for metabolites showing ≥2-fold changes. The anthocyanin fraction remarkably reduced the growth ofE. coliat 4 h by 95.8 and 99.9 % at minimum inhibitory concentration (MIC) and 2× MIC, respectively. The anthocyanin fraction (MIC) had a bacteriostatic effect and was shown to have perturbed glycerophospholipids (1-acyl-sn-glycero-3-phosphoethanolamine, phosphatidylglycerol, diacylglycerol and cardiolipin), amino acids (valine, tyrosine and isoleucine) and energy (ubiquinone and NAD) metabolites at 1 and 4 h. This study demonstrated significant metabolic perturbations of the glycerophospholipid, amino acid and energy metabolism, with these being the key pathways involved in the bacteriostatic activity of anthocyanins fromC. ternatea, which may have promise as bacteriostatic agents forE. coli-related infections.