Effective biosafe management strategies are used to decrease world crop damage produced by plant-parasitic nematodes. This study evaluated the efficiency of hydroxyapatite nanoparticles (n-HAP) and mycorrhizal fungi to control the Meloidogyne incognita infecting tomato plants. Application of n-HAP significantly increased the juveniles’ mortality (195.67%) and egg hatching inhibition percentage (80.71%) compared to the untreated control, in vitro. Mycorrhizal and/or n-HAP treatments increased the plant growth parameters (root and shoot length, dry weight, and leaf area) and reduced the negative consequence of nematode infection. This may be due to indirect mechanisms through increasing plant nutrient uptake efficiency and increasing the internal plant resistance against nematode infection. In dual-treated plants, phosphorus, nitrogen, and calcium content recorded the highest value in the nematode-infected plants. Whereas the dual inoculation significantly increased mineral contents in tomato plants compared with control, this may induce the strength of the cell wall of the epidermal layer and cortex and consequently increase the plant resistance against nematode infection. Our results revealed that the application of the plant resistance-stimulants enhanced the plant growth parameters and internal nutrient content and reduced the nematode’s criteria. Consequently, the internal plant resistance against nematode infection was induced.