Using integrated pest management without relying on chemical pesticides is one of the most attractive approaches to control plant pathogens. Among them, using resistant cultivars or rootstocks against diseases in combination with beneficial microorganisms has attracted special attention. The citrus nematode is one of the major constraints of citrus cultivation worldwide. We showed that the mycorrhizal arbuscular fungus, Funneliformis mosseae, increases growth parameters including shoot and root length and biomass of two main rootstocks of citrus, sour orange and Volkamer lemon, in non-infected and infected plants with citrus nematode. It decreased the infection rate by citrus nematode in both rootstocks compared with non-mycorrhizal plants. The rate of decrease in nematode infection was highest when plants were pre-inoculated with F. mosseae and was lowest when nematode was inoculated before F. mosseae. However, when nematode was inoculated before the fungus, the fungus was still able to mitigate the negative effect of infection by nematode compared with plants inoculated with nematode only. This suggests that the timing of inoculation plays a crucial role in the effectiveness of F. mosseae in reducing nematode infection. Moreover, monitoring of the expression of two genes, phenylalanine ammonia-lyase (PAL) and β-1,3-Glucanase which are involved in systemic acquired resistance (SAR) showed that although they were significantly upregulated in mycorrhizal plants compared with non-mycorrhizal plants, they showed the highest expression when plants were pre-treated with fungus before nematode inoculation thus indicating that plants were primed. In summary, F. mosseae primes the defense-related genes involved in SAR, increasing plant defensive capacity and boosting citrus rootstock growth parameters has important implications for the agricultural industry.