‘Kinnow’ Mandarin is highly prone to quality deterioration during postharvest storage which seriously affects consumer acceptability. In order to understand the biochemical basis for alterations in quality, a comprehensive evaluation of various metabolites was undertaken by storing fruits at low temperature (5°C) and ambient temperature (20°C) for 8 and 4 weeks, respectively. Sugars, organic acids, vitamins, polyphenolic, and limonoids were quantified through LC-MS/MS. While concentrations of glucose and fructose showed an increasing trend at ambient temperature; values reached a plateau by 14 days at low temperature. Organic acids, vitamin-B complex and C declined significantly during storage; however, the pattern of decline was more rapid at ambient temperature than low temperature. High limonin levels were observed in fruits stored at ambient temperature. Based on metabolites, it seems that ‘Kinnow’ fruits can be safely stored for 6 weeks at low temperature without any impairment in quality. Overall results strongly suggest that both duration and temperature of storage are essential in determining optimum shelf life. Thus, metabolite profiling is a useful tool for discriminating differences in metabolites of citrus fruits stored under different storage conditions.