The Salvia genus, particularly the wild genotypes, received significant attention due to its antibacterial, antioxidant, antiviral, and anticancer properties. Crossbreeding wild and cultivated plants can conserve the genetic resources of wild plants and develop new hybrids with high yields and high resistance to climatic changes. In this study, Salvia multicaulis (P1, wild) and Salvia officinalis (P2, cultivated) have been crossed to produce a novel hybrid (F1 hybrid) in the Saint Catherin protectorate - Egypt. In P1, P2, and F1 hybrid, heterosis, phytochemical composition, gene expression of PAL (Phenylalanine ammonia-lyase), RAS1 (Rosmarinic acid synthase I), CYP (Cytochrome P450), and CS (1,8-Cineole synthase), besides antioxidant, anticancer, anti-inflammatory, and antibacterial effects were assessed. The F1 hybrid recorded the highest means of plant height in the two seasons. Heterosis over the mid-parents was positively associated with various traits, including stem thickness, number of branches, fresh yield, and percentage of oil in both seasons. Total phenolic and flavonoid content were found in the following order: P2 > P1 > F1. DPPH antioxidant effect was found in the following order: P2 > F1 > P1. The F1 hybrid had the highest content of rosmarinic acid (12.379 mg/g), quercetin (0.595 mg/g), and naringenin (0.152 mg/g), followed by P1 and P2. The 1,8-cineol and α-pinene were the main compounds in the essential oils of P1, P2, and F1. The 1,8-cineol was found in the following order: P2 > F1 > P1, while α-pinene was found in the following order: P1 > F1 > P2. The RAS1 expression showed a weak correlation with the concentration of rosmarinic acid, while the expressions of PAL and CYP were strongly correlated with the concentrations of main phenolics, including rosmarinic acid, quercetin, and naringenin. The 1,8-cineol content was negatively correlated with the expression of the CS gene. The P2 extract and the F1 hybrid essential oil showed potent anticancer, anti-inflammatory, and antibacterial properties. Crossbreeding S. multicaulis (P1, wild) and S. officinalis (P2, cultivated) in this study developed a new hybrid (F1) with good growth characteristics, high essential oil yields, high levels of bioactives, and good bioactivity. This makes it suitable for large-scale production for use in food and pharmaceutical applications.