Human cancer and pathogenic microbes cause a significant number of deaths every year. Modulating current sources of natural products that control such diseases becomes essential. Natural algae, such as Ascophyllum nodosum and Ecklonia maxima, can modulate the metabolic processes as well the bioactivities of Ruta graveolens L. The R. graveolens plants were subjected to nine soil drenches of A. nodosum (7 mL L−1), E. maxima (7 mL L−1), or both extracts. Morphological performance, gas exchange parameters, and essential oils (EOs) composition (GC-MS) were studied and the bioactivity was assessed against several cancer cells and pathogenic bacteria or fungi. Treatment with A. nodosum + E. maxima seaweed extracts (SWE) led to the highest morphological performance and gas exchange parameters. The highest antiproliferative, apoptotic, and caspase-3/7 activities of EO were against HeLa in SWE mixture treated plants. The best EO antimicrobial activities were obtained against Staphylococcus aureus and Penicillium ochrochloron. SWE mixtures treated plants showed the best bioactivities against microbes and cancer cells. The highest abundance of 2-undecanone (62%) and 2-nonanone (18%) was found in plants treated with SWE mixtures and caused the best anticancer and antimicrobial effects. Seaweed mixtures act as natural elicitors of pharmaceutical industries and favored 2-undecanone and 2-nonanone in R. graveolens.