BACKGROUND Juglans regia Linn. and Carya illinoinensis (Wangenh.) K. Koch are nut-producing plant species of the Juglandaceae family. Bioactive compounds like naphthoquinones, tetralones, and diarylheptanoids are dominant in these species. OBJECTIVE The study aimed to develop and validate a fast and sensitive analytical method by ultrahigh-performance liquid chromatography diode array detection mass spectrometry (UHPLC-DAD-MS) for quantification and identification of bioactive compounds in fruit pericarps and leaves of J. regia and C. illinoinensis collected from two different states of north India. METHODS The dried pericarps of J. regia and C. illinoinensis (500 mg) were extracted with ethyl acetate-methanol (50:50 v/v, 20 mL, 50°C, 30 min) by ultrasonication and analysed by ultrahigh-performance liquid chromatography diode array detection quadrupole time-of-flight tandem mass spectrometry (UHPLC-DAD-QTOF-MS/MS) for qualitative and quantitative examination of phytoconstituents. The method was validated according to International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human use (ICH) guidelines for linearity, precision, accuracy, limit of detection (LOD), and limit of quantification (LOQ). RESULTS Here, we report the quantification of dihydrophaseic acid (1), 4,5-dihydroxytetralone (2), 4,8-dihydroxytetralone (3), 5,8-dihydroxy-3-methoxytetralone (4), and juglanin A (5) in the pericarps and leaves of J. regia and C. illinoinensis. Furthermore, using the hyphenated analytical method, a total of 62 compounds were tentatively characterised in different samples. The principal component analysis (PCA) showed diversity between the analysed sample's composition. Also, the study evaluated the variation of bioactive compounds among different parts of J. regia and C. illinoinensis collected from different regions of northern India by UHPLC-DAD-QTOF-MS/MS. CONCLUSIONS The developed method is simple, rapid, and selective for the identification and characterisation of bioactive molecules.