The integration of green natural chemical resources in agricultural, industrial, and pharmaceutical applications allures researchers and scientistic worldwide. Cleome amblyocarpa has been reported as an important medicinal plant. However, its essential oil (EO) has not been well studied; therefore, the present study aimed to characterize the chemical composition of the C. amblyocarpa, collected from Egypt, and assess the allelopathic, antioxidant, and anti-inflammatory activities of its EO. The EO of C. amblyocarpa was extracted by hydrodistillation and characterized via gas chromatography–mass spectrometry (GC-MS). The chemometric analysis of the EO composition of the present studied ecospecies and the other reported ecospecies was studied. The allelopathic activity of the EO was evaluated against the weed Dactyloctenium aegyptium. Additionally, antioxidant and anti-inflammatory activities were determined. Forty-eight compounds, with a prespondence of sesquiterpenes, were recorded. The major compounds were caryophyllene oxide (36.01%), hexahydrofarnesyl acetone (7.92%), alloaromadendrene epoxide (6.17%), myrtenyl acetate (5.73%), isoshyobunone (4.52%), shyobunol (4.19%), and trans-caryophyllene (3.45%). The chemometric analysis revealed inconsistency in the EO composition among various studied ecospecies, where it could be ascribed to the environmental and climatic conditions. The EO showed substantial allelopathic inhibitory activity against the germination, seedling root, and shoot growth of D. aegyptium, with IC50 values of 54.78, 57.10, and 74.07 mg L−1. Additionally, the EO showed strong antioxidant potentiality based on the IC50 values of 4.52 mg mL−1 compared to 2.11 mg mL−1 of the ascorbic acid as standard. Moreover, this oil showed significant anti-inflammation via the suppression of lipoxygenase (LOX) and cyclooxygenases (COX1, and COX2), along with membrane stabilization. Further study is recommended for analysis of the activity of pure authentic materials of the major compounds either singularly or in combination, as well as for evaluation of their mechanism(s) and modes of action as antioxidants or allelochemicals.