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Plasmodium falciparum is one of the parasites responsible for malaria, a serious and potentially deadly disease. Mitragyna inermis, a plant used to treat malaria in Africa, shows antiplasmodial activity against P. falciparum. Its extracts may target Lactate Dehydrogenase and Protein Kinase G, two enzymes crucial for the parasite’s survival, but the impact of certain pure molecules such as quinovic acid glycosides on these enzymes remains to be determined. To isolate, characterize and evaluate M. inermis compounds for their potential to inhibit Plasmodium LDH and cGMP-dependent protein kinase enzymes through experimental and computational approaches. Phytochemical investigation was conducted using chromatographic techniques, and compounds structures were elucidated by ESI-MS and comprehensive 1&2D NMR analyses. Antiplasmodial activity was assessed on Dd2/3D7 mutant strains. In silico analyses included molecular docking, ADMET prediction, and 100-ns molecular dynamics simulations against LDH and cGMP-dependent protein kinase. Five compounds were isolated and structurally characterized from the stem bark of M. inermis: quinovic acid 3-O-β-D-fucopyranoside (1), quinovic acid 3-O-β-D-glucopyranoside (2), quinovic acid 3-O-β-D-fucopyranosyl-(28→1)-β-D-glucopyranosyl ester (3), olean-12-ene-3β,19β,24-triol (4), and lupeol-3-O-undecanoate (5). Compounds 4 and 5 are reported for the first time from the genus Mitragyna. Compound 3 demonstrated the highest antiplasmodial activity against both PfDd2 and Pf3D7 strains, and exhibited the strongest binding affinity toward PfLDH (−8.2 kcal/mol). MD simulations further confirmed the stability of the C3_PfLDH complex throughout the 100 ns simulation period. These results provide phytochemical and pharmacological support for the ethnomedical use of M. Inermis stem bark for malaria treatment and expand the chemotaxonomic knowledge of the genus Mitragyna.