This work aims to study the variations in the composition of Lantana camara leaf, flower, and stem essential oils over two years. L. camara organs were harvested in Bregbo (East Côte d’Ivoire) each month from June 2015 to June 2017. The essential oils were obtained by hydrodistillation and characterized by GC-MS and 13C NMR. Eighty-four compounds accounting for 84.4–99.1% of the essential oils have been identified. The essential oils hydrodistillated from L. camara are dominated by sesquiterpenes such as (E)-β-caryophyllene and α-humulene, which were found in all samples. Some monoterpenes such as thymol, sabinene, and α-pinene were also present. Statistical analysis (principal component analysis and clustering) revealed a high variability in essential oil composition between the different organs and also within the studied periods, as the thymol proportion was higher during flowering and fruiting months. In addition, the stem, flower, and fruit essential oils were more concentrated in thymol than the leaf essential oils. The proportions of (E)-β-caryophyllene and α-humulene were strictly inverted with the thymol proportion throughout the harvest period or vegetative cycle. The antioxidant, anti-inflammatory and insecticidal activities of leaves and flowers essential oils were also studied. Results showed that L. camara leaf and flower essential oils displayed high antioxidant, anti-inflammatory and insecticidal activities.