Background Due to its medicinal properties, Pistacia integerrima is in high demand and is extensively used as a key ingredient in various formulations. However, its popularity has led to IUCN threatened category list. In Ayurvedic texts, such as Bhaishajaya Ratnavali, Quercus infectoria is recommended as a substitute for P. integerrima in different formulations. Additionally, Yogratnakar highlights that Terminalia chebula shares similar therapeutic properties with P. integerrima. Objective The objective of the current study was to gather scientific data on metabolite profiling and markers-based comparative analysis of Q. infectoria, T. chebula and P. integerrima. Methods In present study, hydro-alcoholic and aqueous extracts of all three plants were prepared and standardized for the comparative evaluation of secondary metabolites. Thin-layer chromatography was carried out for the comparative fingerprinting of the extracts using chloroform: methanol: glacial acetic acid: water (60: 8: 32: 10, v/v/v/v) as a solvent system. A fast, sensitive, selective, and robust HPLC method was developed to determine gallic acid and ellagic acid from both extracts of all three plants. The method was validated for precision, robustness, accuracy, limit of detection and quantitation as per the International Conference on Harmonization guidelines. Results The TLC analysis revealed the presence of several metabolites, and the pattern of metabolites in the plants exhibited a certain degree of similarity. A highly precise and reliable quantification technique was created for gallic acid and ellagic acid, operating within the linear concentration range of 81.18–288.22 µg/mL and 3.83–13.66 µg/mL, respectively. The correlation coefficients for gallic acid and ellagic acid were 0.999 and 0.996, indicating strong relationships. The gallic acid content in all three plants ranged from 3.74% to 10.16% w/w, while the ellagic acid content ranged from 0.10% to 1.24% w/w. Conclusions This pioneering scientific approach highlights the phytochemical similarities between Q. infectoria, T. chebula and P. integerrima.