Essential oils (EOs) and Plant extracts (PEs) are gaining attention as eco-friendly alternatives to synthetic fungicides for the management of soil-borne fungi related to root rot and the wilt of marigolds. Here, EOs of Cinnamomum zeylanicum (cinnamon), Mentha piperita (peppermint), Syzygium aromaticum (clove), Thymus vulgaris (thyme), PEs of Cymbopogon citratus (lemongrass), Lantana camara (lantana), Ocimum basilicum (basil), and Zingiber officinales (ginger) were first evaluated in vitro for their inhibitory activity against the mycelium growth of the root rot and wilt fungi of marigold: Rhizoctonia solani, Sclerotinia sclerotiorum, Fusarium oxysporum, and F. solani, and in vivo for their activity in reducing disease progression. The results show that all EOs had a strong inhibitory activity on the mycelium growth of pathogens. Maximum inhibition of mycelium growth was achieved at a concentration of 1 mL/Lof S. aromaticum, C. zeylanicum, and M. piperita. The inhibition values were 100, 80.9, and 72.4% for F. solani, 100, 81.1, and 70% for S. sclerotiorum, 90.2, 79.4, and 69.1% for F. oxysporum, and 85.4, 78.2, and 68.7% for R. solani, respectively. Regarding plant extracts, the highest inhibition of mycelium growth was attained at a concentration of 20% of Z. officinales, C. citratus, and L. camara. The inhibition values were 77.4, 69.1, and 60.6% for F. solani, 76.5, 67.2, and 58% for S. sclerotiorum, 73.5, 68.2, and 56.3% for F. oxysporum, and 72, 64.8, and 55.2% for R. solani, respectively. In pot experiments, the application of EOs and PEs showed high efficiency in suppressing root rot and wilt of marigold at all concentrations used, especially at 3 mL/L for seed soaking (along with 1.5 mL/L for foliar spraying) for S. aromaticum, C. zeylanicum, and M. piperita EOs, and (40% for seed soaking along with 20% for foliar spraying) for Z. officinales, C. citratus, and L. camara PEs. All the treatments applied in the field greatly reduced the diseases in both seasons, especially S. aromaticum EO, C. zeylanicum EO, Z. officinales PE, and carbendazim treatments. This was accompanied by a significant improvement in morphological, yield, and phytochemical parameters of marigold as well as a significant increase in the activity of defense-related antioxidant enzymes. Overall, essential oils and plant extracts can be used effectively to control root rot and wilt in marigold as sustainable and eco-friendly botanical biofungicides.