To elucidate how biosynthesis of plant metabolites is affected by temperature, metabolite profiles from in vitro regenerated plants raised under different temperature regimes of 10, 15 °C, 20 °C, 25 °C and 30 °C were obtained using electrospray ionization mass spectrometry (ESI-MS), and principal component analysis (PCA) was carried out to identify key metabolites. Several bin masses were detected by PCA loading scatter plots which separated the samples. In-house bin program selectively manifested the putative known metabolites depending on % total ions count and intensity of selected bins in the plant samples. Total phenolic and flavonoid content were harvested to highest levels (12.9 mg GAE/g DW and 9.3 mg QE/g DW), respectively, at 15 °C. Besides, pinoresinol (lignan), some of the vital amino acids such as serine, methionine, histidine and glutamine were found to be at higher amount in plants raised at 15 °C. Significant phenylpropanoids like cinnamic acid, caffeic acid and quercitol were detected at a higher concentration in plants raised at 15 °C as compared to other treatments. However, phosphoenolpyruvate, and oxalosuccinate (intermediates of the pentose phosphate pathway) were accumulated the most in plants raised at 30 °C and they were detected with lowest values at 10 °C. Glucose and deoxy-xylose 5 phosphate (intermediates of TCA cycle) were found in higher amounts at temperature treatments of 15 and 25 °C, respectively. We conclude that a low-temperature treatment (15 °C) results in a stress-induced accumulation of a variety of pharmacologically important secondary metabolites.