This study focused, for the first time, on the evaluation of the seasonal effect on the chemical composition and biological activities of essential oils hydrodistillated from leaves, trunk bark and fruits of Zanthoxylum leprieurii (Z. leprieurii), a traditional medicinal wild plant growing in Côte d’Ivoire. The essential oils were obtained by hydrodistillation from fresh organs of Z. leprieurii growing on the same site over several months using a Clevenger-type apparatus and analyzed by gas chromatography-mass spectrometry (GC/MS). Leaf essential oils were dominated by tridecan-2-one (9.00 ± 0.02–36.80 ± 0.06%), (E)-β-ocimene (1.30 ± 0.50–23.57 ± 0.47%), β-caryophyllene (7.00 ± 1.02–19.85 ± 0.48%), dendrolasin (1.79 ± 0.08–16.40 ± 0.85%) and undecan-2-one (1.20 ± 0.03–8.51 ± 0.35%). Fruit essential oils were rich in β-myrcene (16.40 ± 0.91–48.27 ± 0.26%), citronellol (1.90 ± 0.02–28.24 ± 0.10%) and geranial (5.30 ± 0.53–12.50 ± 0.47%). Tridecan-2-one (45.26 ± 0.96–78.80 ± 0.55%), β-caryophyllene (1.80 ± 0.23–13.20 ± 0.33%), α-humulene (4.30 ± 1.09–12.73 ± 1.41%) and tridecan-2-ol (2.23 ± 0.17–10.10 ± 0.61%) were identified as major components of trunk bark oils. Statistical analyses of essential oil compositions showed that the variability mainly comes from the organs. Indeed, principal component analysis (PCA) and hierarchical cluster analysis (HCA) allowed us to cluster the samples into three groups, each one consisting of one different Z. leprieurii organ, showing that essential oils hydrodistillated from the different organs do not display the same chemical composition. However, significant differences in essential oil compositions for the same organ were highlighted during the studied period, showing the impact of the seasonal effect on essential oil compositions. Biological activities of the produced essential oils were also investigated. Essential oils exhibited high insecticidal activities against Sitophilus granarius, as well as antioxidant, anti-inflammatory and moderate anti-plasmodial properties.