Lung and ovarian cancers account for substantial cancer morbidity and mortality worldwide. Plant-derived natural products represent promising alternatives in cancer therapy because of their structural diversity and ability to target multiple signaling pathways. Prosopis species are ethnomedicinal plants traditionally known for their antimicrobial, anti-inflammatory, and antioxidant activities; however, their anticancer potential remains poorly explored. This study evaluates the anticancer properties of extracts of Prosopis cineraria, Prosopis farcta, and Prosopis juliflora, the Prosopis species growing in Qatar, against human lung (A549) and ovarian (SK-OV-3) cancer cells. Gas chromatography–mass spectrometry (GC–MS) was used to characterize their phytochemical composition. The cytotoxicity and anti-migratory activity of the three extracts were evaluated. Western blot analysis was performed to investigate the molecular effects of the extracts on proliferation- and apoptosis-related proteins. GC–MS profiling identified diverse low-molecular-weight bioactive compounds across the extracts, including several compounds detected only in P. juliflora, which exhibited the most potent cytotoxicity toward A549 and SK-OV-3 cells. All three extracts inhibited cancer cell migration, with P. juliflora showing the strongest effect. Furthermore, P. juliflora reduced the expression of proliferation and survival markers and increased the expression of pro-apoptotic proteins. These findings identify P. juliflora as the most active of the three tested Prosopis extracts and support further investigation of its in vitro anticancer potential.