The potential of plant-based natural compounds in the creation of new molluscicidal and antimicrobial medications has gained attention in recent years. The current study compared the metabolic profiles, antibacterial, and molluscicidal properties of the medicinal plants Calotropis procera (C. procera) and Atriplex halimus (A. halimus). In both plants, 118 metabolites were identified using gas chromatography-mass spectrometry. Palmitic acid, stigmasterol, and campesterol were the most prevalent constituents. C. procera extract showed stronger antibacterial activity than A. halimus against Escherichia coli and Proteus mirabilis. Both extracts exhibited molluscicidal activity against Biomphalaria alexandrina, with LC50 values of C. procera (135 mg/L) and A. halimus (223.8 mg/L). Survival rates of snails exposed to sub-lethal concentrations (LC25) of C. procera and A. halimus extracts were 5% and 20%, respectively. The hatchability of snail eggs exposed to both extracts has been dramatically reduced. Both extracts significantly decreased the levels of alkaline phosphatase, acid phosphatase, total protein, and albumin in snails, as well as causing DNA damage and resulting in numerous hermaphrodite and digestive gland damages and distortions. Molecular docking showed palmitic acid binding with acid, alkaline, and alanine aminotransferases in treated digestive gland snails. In conclusion, C. procera and A. halimus have antibacterial and molluscicidal properties.