Pitaya ( genus) is a popular plant with exotic and nutritious fruit, which has widespread uses as a source of nutrients and raw materials in the pharmaceutical industry. However, the potential of pitaya peel as a natural source of bioactive compounds has not yet fully been explored. Recent advances in metabolomics have paved the way for understanding and evaluating the presence of diverse sets of metabolites in different plant parts. This study is aimed at exploring the diversity of primary and secondary metabolites in two commercial varieties of pitaya, i.e., green pitaya () and red pitaya (). A total of 433 metabolites were identified using a widely targeted metabolomic approach and classified into nine known diverse classes of metabolites, including flavonoids, amino acids and its derivatives, alkaloids, tannins, phenolic acids, organic acids, nucleotides and derivatives, lipids, and lignans. Red pitaya peel and pulp showed relatively high accumulation of metabolites viz. alkaloids, amino acids and its derivatives, and lipids. Differential metabolite landscape of pitaya fruit indicated the presence of key bioactive compounds, i.e., L-tyrosine, L-valine, DL-norvaline, tryptophan, -linolenic acid, and isorhamnetin 3-O-neohesperidoside. The findings in this study provide new insight into the broad spectrum of bioactive compounds of red and green pitaya, emphasizing the valorization of the biowaste pitaya peel as raw material for the pharmaceutical and food industries.