The metabolite profiling of extracts from Adansonia digitata L. (baobab) fruit pulp and leaf, and the quantification of their major components, was conducted by means of reverse-phase, high-performance liquid chromatography with photodiode array detection, coupled to electrospray ion-trap mass spectrometry (RP-HPLC-PDA-ESI-MS/MS) and high field nuclear magnetic resonance (NMR) spectroscopy. Water-soluble metabolites from chemical classes including sugars, amino acids, organic acids, and phenolic compounds, were identified, in addition to metabolites soluble in organic solvents such as triacylglycerides, sterols, and fatty acids, and most of these were quantified. The profiling of the primary and secondary metabolites of baobab fruit and leaves addresses the limited knowledge of the chemical composition of baobab, and helps support and explain the growing evidence on its nutritional and biological properties, and provide suggestions about the possible uses of baobab fruit and leaves by food, pharmaceutical and cosmetic industries.