The use of natural products as an alternative for the control of agricultural pests has stimulated the search for new phytosanitary products from nature. The essential oils of Xylopia aromatica (Annonaceae) display a potential repellent action against the whitefly (Bemisia tabaci), a highly important agricultural pest in agriculture worldwide affecting several crops, including tomatoes. Remarkably, the nanoencapsulation of the active compounds of essential oils promotes not only their protection against environmental degradation but also prolongs their activity through the gradual release. However, pesticide risk assessments to release novel phytosanitary products in the market include experiments designed to measure the effect of pesticides on the target plant, ensuring the required yield by the agricultural sector. Thus, here we investigated the physiological and metabolic impacts in tomato plants (Solanum lycopersicum L.) submitted to the application of essential oils of X. aromatica. To this end, we used 4-week-old tomato plants and applied in natura and nanoencapsulated essential oils of leaves and fruits at the concentrations of 1 and 2%. The essential oils were obtained by hydrodistillation and presented as the major compounds limonene (37.76%), bicyclogermacrene (13.59%), α-pinene (7.75%) and β-pinene (8.11%) for essential oils of leaves whereas limonene (65.44%), β-pinene (8.44%), α-pinene (7.66%) and β-myrcene (3.29%) are the major compounds in essential oils for fruits. The nanoencapsulation of the essential oils in polymeric matrix (PCL) presented smooth and monodisperse nanoparticles with encapsulation efficiency between 94 and 98%. Our results revealed that the application of the essential oils did not lead to physiological damage to the tomato plants as observed by the absence of changes in both gas exchange and chlorophyll fluorescence a parameters. Moreover, changes in height, total leaf area and specific leaf area, leaf dry mass, dry mass and biomass allocation were not observed. Furthermore, no significant changes were observed in the sugars (sucrose, glucose and fructose), starch, malate, chlorophyll a and b, amino acids, proteins and nitrate. Taken together, the data obtained indicate that the application of essential oils of leaves and fruits of X. aromatica, either in natura or nanoencapsulated, does not negatively impact growth and metabolism of tomato plants. We posit that the association of nanotechnology with the usage of natural products is potentially advantageous for the agricultural sector in pest management, although pesticide risk assessments should be performed.