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The aim of this study was to investigate the metabolic changes associated with the anti-obesity effects of fermented blackberry extracts in the liver tissues of high-fat-diet-fed mice using mass spectrometry-based metabolomics analysis. C57BL/6J mice were divided into eight groups: normal-diet-fed mice, high-fat-diet-fed mice, high-fat diet treated with blackberry extract, high-fat-diet mice treated with blackberry fermented by <i>L. plantarum</i>, and high-fat diet with blackberry fermented by <i>L. brevis</i>. After 12 weeks, the high-fat-diet group exhibited a greater increase in liver weight compared to the control group, and among the groups, the group administered with blackberry fermented with <i>L. plantarum</i> showed the most pronounced reduction in liver weight. As the primary organ responsible for amino acid metabolism, the liver is crucial for maintaining amino acid homeostasis. In our study, we observed that the levels of several essential amino acids, including isoleucine and valine, were decreased by the high-fat diet, and were recovered by administration of blackberry extract fermented with <i>L. plantarum</i>. Our results demonstrated the potential of blackberry extract fermented with <i>L. plantarum</i> as a functional material for metabolic disorders by restoring some of the amino acid metabolism disturbances induced by a high-fat diet.