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Introduction: Goat milk has poorer fermentation characteristics due to the absence or only traces of αs1-casein, due to which goat yoghurt contains a less dense gel structure. Moreover, the fermentation characteristics of the milk vary between the breeds of the same species. Therefore, it becomes imperative to explore a few metabolites which could regulate the techno-functional properties of goat yoghurt. Objectives: This study was aimed at relating the metabolite profile of yoghurt prepared from milk of <i>Barbari</i>, an indigenous goat breed of India, and its techno-functional properties (firmness, whey syneresis, and flow behaviour) using multivariate data analysis and regression models. Results: Goat yoghurt was prepared with two different total solids (TS) levels (12 and 16%) and cultures, namely, commercial culture comprising a thermophilic yoghurt culture (A) and NCDC-263 comprising a mixed yoghurt culture (B). Results demonstrated a significant difference (<i>p</i> < 0.05) in whey syneresis with the increase in the TS level. Flow behaviour of all yoghurt samples showed a decrease in viscosity with an increase in shear rate, which confirmed its non-Newtonian behaviour and shear thinning nature, whereas frequency sweep confirmed its viscoelastic nature. Firmness was the most affected under the influence of different TS and culture levels. It was higher (<i>p</i> < 0.05) for 16-A, followed by 16-3B, and minimum for 12-2B. GC-MS-based metabolomics of the yoghurt revealed a total of 102 metabolites, out of which 15 metabolites were differentially expressed (<i>p</i> < 0.05), including 2-hydroxyethyl palmitate, alpha-mannobiose, and myo-inositol. Multivariate data analysis revealed clear separation among groups using principal component analysis and several correlations using a correlation heat map. Further, regression analysis exhibited methylamine (0.669) and myo-inositol (0.947) with higher regression coefficients (R² values) exceeding 0.6, thus demonstrating their significant influence on the techno-functional properties, mainly firmness, of the yogurt. Conclusion: In conclusion, A gas chromatography-based metabolomics approach could successfully establish a relationship between the metabolome and the techno-functional properties of the yoghurt.