Watermelon mosaic virus (WMV) is a major constraint in squash production, necessitating sustainable antiviral strategies. This study evaluated the efficacy of aqueous extracts from six medicinal plants: Artemisia sp., Matricaria chamomilla, Allium cepa, Allium sativum, Moringa oleifera, and Citrullus colocynthis in promoting plant growth and mitigating WMV infection. To the best of our knowledge, this is the first report demonstrating the efficacy of the combined application of Artemisia extract and B. mycoides revealed a synergistic effect, significantly enhancing physiological recovery and reducing disease severity compared to single treatments. Treatments were applied through seed soaking, soil inoculation, and foliar spraying in a greenhouse experiment using a randomized complete block design. Growth parameters, chlorophyll content, total soluble carbohydrates, disease severity, and antioxidant enzyme activities (PAL, PPO, CAT, SOD) were measured. A comparative evaluation of multiple application methods (seed soaking, soil inoculation, and foliar spraying) provided critical insights into the most effective delivery strategies for biocontrol agents. Soil inoculation with Artemisia extract yielded the greatest overall reduction in infection levels, outperforming both seed soaking and foliar application methods. Treatments with Artemisia extract and Matricaria chamomilla, applied either through soil or foliar inoculation, significantly improved plant height. Across treatments, systemic infection rates were significantly reduced at p ≤ 0.05, ranging from 21% to 76.6%, depending on the extract and application method. GC–MS analysis of the plant extracts revealed that Moringa and Artemisia exhibited the most significant antiviral potential. Results showed that plant extracts significantly reduced WMV severity, with Artemisia (soil inoculation) lowering disease severity from 90% to 21%. The integrated application of Artemisia extract and B. mycoides produced synergistic effects, with soil inoculation yielding the most consistent physiological and biochemical enhancements. This treatment also improved chlorophyll a, mitigating pigment loss due to WMV. Overall, these findings establish a novel eco-friendly approach for WMV management, integrating microbial and botanical interventions to promote plant resilience.