Background: Stevia (Stevia rebaudiana) is a plant of nutritional and industrial importance for its diverse steviol glycosides. Stevioside, rebaudioside-A and their aglycon steviol – 200-300 times sweeter than normal sucrose are novel contenders for the development of antidiabetic drugs. Stevia leaf flavor at different harvest stages is a function of the metabolite content, which results from physiological changes during plant growth and development. Objectives: The main purpose of this study was to investigate metabolite changes during plant development using GC-MS metabolic profiling and HPTLC and to analyze expression of key genes of steviol glycoside biosynthetic pathway by qPCR. Material Methods: Metabolite data and gene expression from leaf samples of eight developmental stages underwent a variety of chemometric analyses, to identify the true differences between samples. Results: There was a significant increase of steviol from 0.23% to 6.6%, stevioside from 3.3% to 14.23%, rebaudioside-A from 0.826% to 4.99% and (+)-isomenthol showed decrease in concentration from 16.79% to 5.23% with plant growth. srUGTs, srKO, srKS, srKAH, srUGP1, and srDXR increased whereas expression of (+)-srLMS and srNMD decreased with plant progression. Metabolite and gene correlation analysis revealed the interdependencies of individual metabolites and metabolic pathways genes. Conclusion: These results will help in selecting and utilizing the appropriate traits in Stevia crop.