Abstract Phytochemical investigation of dichloromethane neutral phase of stem bark of Nauclea pobeguinii led to the isolation of a new monoterpene indole alkaloid, pobeguinine 1 along with 14 known compounds including (−)-naucleofficine D (2a), (+)-naucleofficine D (2b), naucleidinal (3), quafrinoic acid (4), betulinic acid (5), ursolic acid (6), quinovic acid (7), quinovic acid 3-O-α-L-rhamnopyranoside (8a), quinovic acid 3-O-β-D-fucopyranoside (8b), β-sitosterol (9), β-sitosterol 3-O-β-D-glucopyranoside (10), benzoic acid (11), lacceroic acid (12) and n-heptacosane (13). The structure of compound 1 was unambiguously assigned on the basis of single-crystal X-ray diffraction technique. The Hirshfeld surface analysis was further carried out to quantitatively analyze the role of various types of hydrogen bonding in crystal stability. These structures were elucidated using spectroscopic methods. The isolates were evaluated for their radical scavenging properties as well as inhibitory activities against urease and tyrosinase enzymes with IC₅₀ values ranging from 13.4 to 58.9, 46.0 to 86.7 and 39.4 to 87.1 μg/mL, respectively. Compound 6 exhibited maximum radical scavenging activity with IC₅₀ 13.4 μg/mL, while compound 4 exhibited maximum tyrosinase with IC₅₀ 39.4 μg/mL. All the isolates showed moderate urease inhibition.