Plants are considered green resources for thousands of bioactive compounds. Essential oils (EOs) are an important class of secondary compounds with various biological activities, including allelopathic and antimicrobial activities. Herein, the present study aimed to compare the chemical profiles of the EOs of the widely distributed medicinal plant Calotropis procera collected from Saudi Arabia and Egypt. In addition, this study also aimed to assess their allelopathic and antimicrobial activities. The EOs from Egyptian and Saudi ecospecies were extracted by hydrodistillation and analyzed via GC-MS. The correlation between the analyzed EOs and those published from Egypt, India, and Nigeria was assessed by principal component analysis (PCA) and agglomerative hierarchical clustering (AHC). The allelopathic activity of the extracted EOs was tested against two weeds (Bidens pilosa and Dactyloctenium aegyptium). Moreover, the EOs were tested for antimicrobial activity against seven bacterial and two fungal strains. Ninety compounds were identified from both ecospecies, where 76 compounds were recorded in Saudi ecospecies and 33 in the Egyptian one. Terpenes were recorded as the main components along with hydrocarbons, aromatics, and carotenoids. The sesquiterpenes (54.07%) were the most abundant component of EO of the Saudi sample, while the diterpenes (44.82%) represented the mains of the Egyptian one. Hinesol (13.50%), trans-chrysanthenyl acetate (12.33%), 1,4-trans-1,7-cis-acorenone (7.62%), phytol (8.73%), and myristicin (6.13%) were found as the major constituents of EO of the Saudi sample, while phytol (38.02%), n-docosane (6.86%), linoleic acid (6.36%), n-pentacosane (6.31%), and bicyclogermacrene (4.37%) represented the main compounds of the Egyptian one. It was evident that the EOs of both ecospecies had potent phytotoxic activity against the two tested weeds, while the EO of the Egyptian ecospecies was more effective, particularly on the weed D. aegyptium. Moreover, the EOs showed substantial antibacterial and antifungal activities. The present study revealed that the EOs of Egyptian and Saudi ecospecies were different in quality and quantity, which could be attributed to the variant environmental and climatic conditions. The EOs of both ecospecies showed significant allelopathic and antimicrobial activity; therefore, these EOs could be considered as potential green eco-friendly resources for weed and microbe control, considering that this plant is widely grown in arid habitats.