The methanolic and water extracts of Carapa procera leaves and stem barks were screened for their phytochemical content using a multi-technique approach. The extracts were also assessed for their in vitro antioxidant capacity along with their anti-diabetic (α-amylase, α-glucosidase), anti-tyrosinase, anti-elastase and anti-cholinesterase (AChE, BChE) activities. Furthermore, antibacterial and antifungal effects were determined against several bacterial and fungal strains. Data Integration Analysis for Biomarker discovery using Latent components (DIABLO) integrative analysis was conducted on collected data to determine the influence of extraction solvents and plant parts on phytochemical content, antioxidant properties and enzyme inhibitory properties of C. procera samples. Additionally, the major identified compounds were screened as modulators of multiple pathways involved in human diseases via Gene Ontology (GO) enrichment analysis. Results showed that methanolic stem bark extract exhibited the most potent ABTS scavenging, Cu2+ and Fe3+ reducing power, total antioxidant capacity and Fe2+ chelating power and displayed the highest total flavanol content. Methanolic extracts of leaves and stem barks were abounded with phenolics and had the greatest anti-AChE, anti-BChE, anti-tyrosinase and anti-elastase activities. A significant antifungal activity was observed, with the lowest minimum inhibitory concentration and minimum fungicidal values of 0.07 and 0.15 mg/mL, respectively. DIABLO integrative analysis suggested that the phytochemical content and biological activities varied significantly within the plant parts and were influenced by types of solvent used. GO enrichment analysis on the main bioactive compounds showed modulation of multiple pathways associated with cancer. Obtained results demonstrated that stem bark and leaves of C. procera can be considered as promising sources of bioactive molecules with high pharmacological values.