The present study investigated the effects of the endophytic fungus, Penicillium pinophilum EU0013 on fruit phytochemical indices and essential trace elements in five tomato cultivars. In a completely randomized design, inoculated and uninoculated seedlings of tomato cultivars (Momotaro, Rodeo, Anaya, Reika, and Cherry) were raised for sixteen weeks in a greenhouse. Fruit fresh weights and root colonization by P. pinophilum were significantly higher in the Rodeo cultivar than in the other cultivars tested. Significant effects of the cultivar, inoculation, and interaction on fruit dry weights were‍ ‍observed with higher values in Anaya inoculated with P. pinophilum. Cultivar and inoculation effects were significant for ascorbic acid and soluble sugars in four cultivars, with increases being observed due to the P. pinophilum inoculation. Lycopene levels increased in Rodeo and decreased in Anaya, while β-carotene levels increased in four cultivars due to the inoculation. Manganese concentrations were significantly increased in Cherry, while iron concentrations were increased in Reika and Cherry. Increases due to the inoculation were observed for gibberellic acids (GA₁ and GA₄) in Reika and Anaya, whereas decreases were detected in Cherry and Rodeo. Similar results were obtained for abscisic acids (ABA) with increases in Reika and Anaya due to the inoculation. P. pinophilum EU0013 demonstrated the ability to improve the nutritive value of tomato fruits via modulations to phytochemicals in addition to increases in Mn and Fe concentrations, particularly in Cherry and Rodeo. Cultivar responses to the P. pinophilum inoculation are a factor that need to be considered for its use in increasing fruit quality indices in tomato.