Plants serve as reservoirs of bioactive compounds endowed by nature, rendering them promising subjects for investigating chemical diversity. Despite their potential, much remains untapped, whether in standardized extracts or isolated pure compounds. This unexplored terrain has paved the way for significant discoveries in pharmaceuticals. Notably, research has delved into the medicinal properties of Mallotus philippensis, a prominent plant in South Asia. Employing meticulous extraction techniques such as maceration, the fruit of this plant underwent initial antimicrobial screening, revealing encouraging results. Subsequent fractionation of the plant’s extracts via liquid–liquid extractions, utilizing dichloromethane and absolute ethanol, facilitated further analysis. Evaluating these fractions for antibacterial activity demonstrated efficacy against various pathogenic microorganisms, particularly Pseudomonas aeruginosa and Escherichia coli, notably by the ethanolic and dichloromethane extracts. Furthermore, a comprehensive phytochemical analysis unveiled the presence of alkaloids, flavonoids, saponins, glycosides, phenols, and tannins. An assessment of the extracts’ antioxidant potential via the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assay showcased significant activity, with a radical scavenging rate of 97%. This underscores the significance of utilizing fruit remnants, which are often rich in valuable chemical constituents yet commonly discarded, thereby adding value to both the species and the environment. Further investigation focused on the composition of Mallotus philippensis fruit, encompassing volatile and non-volatile metabolites through HPLC-MS analysis. Additionally, this study introduced the application of ionic liquid-loaded polysulfone microcapsules to enrich target constituents from crude extracts. An exploration of the key separation conditions, results, and recycling performance of these microcapsules provided insights for future research endeavors. Overall, this comprehensive study of Mallotus philippensis fruit extracts establishes a foundation for the ongoing exploration and development of this medicinal plant.