Aegle marmelos Correa (Bael tree) is a medicinal fruit tree, widely used for healing purposes in various systems of medicines. Coumarins and alkaloids present in various parts of bael tree including roots and fruit pulp are the primary active constituents implicated for its biological activities. An efficient liquid chromatography–electrospray ionization—tandem mass spectrometry (LC—ESI—MS/MS) method was developed for identification and simultaneous determination of four coumarin derivatives, namely, umbelliferone, psoralene, marmin, and imperatorin, and an alkaloid, skimmianine, in root and stem bark of A. marmelos. The chromatographic separation of analytes was performed on Altima C18 (50 × 4.6 mm, 3 μm) column using methanol and 0.1% acetic acid in water (54:46, v/v) as the mobile phase under isocratic conditions. The LC–MS/MS parameters were optimized in the positive ionization mode using electrospray ionization source. The quantification of the analytes was performed using multiple reaction monitoring (MRM) transitions, umbelliferone (m/z 163.1 → 107.1), psoralene (m/z 187.2 → 131.1), marmin (m/z 333.5 → 163.2), imperatorin (m/z 271.1 → 203.1), and skimmianine (m/z 260.1 → 227.0). The extraction method was standardized for optimum yield of coumarin derivatives and the alkaloid in different extraction solvents. Higher yield of the analytes was found in methanolic extracts in comparisons to petroleum ether, chloroform, ethyl acetate, ethanol, and water. The method was validated for linear range, intra- and inter-batch precision and accuracy. The distribution of coumarin derivatives and an alkaloid was found to vary significantly in different plant samples, and their concentration was much higher in roots as compared to stem bark.