Root rot is one of the most deadly diseases that affect faba bean plants. This study proved the effectiveness of chitosan, chitosan nanoparticles (chitosan NPs), and arbuscular mycorrhizal fungi (AMF) as a secure substitute and a method of control against root rot disease caused by Fusarium oxysporum. It also enhanced the physiological characteristics of faba bean plants and their capacity to directly inhibit pathogens or induce them to fight diseases. Arbuscular mycorrhiza, chitosan NPs, and chitosan all have the power to promote plant growth. They have an impact on a variety of physiological functions in plants, such as nutrient intake, cell division, enzyme activation, growth parameters, mineral content, photosynthetic pigments, and the production of phenol and total soluble sugar, which leads to increased yield. Also, this study demonstrated that chitosan NPs have higher antifungal effects than chitosan and are more effective when combined with mycorrhizal fungi than without them. In addition, a low concentration of chitosan NPs has a higher effect than a high concentration.