The tomato plant is usually infected with various pathogens such as pests, bacteria, and different mycoflora. In this investigation, Tomato plant cultivar Beeli was pathogenized with Fusarium oxysporum f.sp. Lycopersicon (F_OL1) fungi. The F_OL1 fungus was controlled by inoculating the pathogenized Tomato plants with each one of the biocontrol microorganisms, such as Arbuscular mycorrhiza (AM), Trichoderma harzianum (T. harzianum), and microbial blend, named as Effective Microorganisms (EM). Consequently, the effect of these biocontrol microorganisms on the amount of chlorophyll, proteins, and defense enzymes of the Tomato plant was estimated. The results showed that the AM, T. harzianum fungi, and “EM” gave similar ameliorative effects. However, there are regulated increasing content of chlorophyll, proteins, and the activities of many protecting compounds such as acid invertase peroxidase. Moreover, these important plant defense mechanisms have a vital role in oxidizing phenolic compounds, which could increase antimicrobial activity. Altogether, the results demonstrate that the protein and chlorophyll are increased differently in all treatments. The protein level is the highest in F_OL1 + EM treatment and the ML showed the highest level of chlorophyll.