Simple Summary This study identified a change in metabolites by fermented blackberries using GC-MS methods in high-fat-diet-induced mice. As a result, the altered metabolites in the high-fat-diet group consisted of 29 metabolites, showing 85% identity with known components in the database. Among the 29 metabolites, essential amino acids, non-essential amino acids, conditionally essential amino acids, and other metabolites were analyzed after treatment with blackberries and fermented blackberries in high-fat-diet-induced mice. This study constitutes a valuable resource on the dietary modification of fermented blackberries for obesity treatment approaches.Abstract 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 L. plantarum, and high-fat diet with blackberry fermented by L. brevis. 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 L. plantarum 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 L. plantarum. Our results demonstrated the potential of blackberry extract fermented with L. plantarum as a functional material for metabolic disorders by restoring some of the amino acid metabolism disturbances induced by a high-fat diet.