Huanglongbing (HLB) reduces the growth and development of citrus and induces changes in secondary metabolites such as flavonoids, limonoids, and polyamines. Likewise, infected plants have a deficient absorption of nutrients such as zinc, potassium, manganese, and copper. Therefore, the objective of this study was to evaluate the influence of different rootstocks on morphology and mineral changes of Citrus limon and Citrus sinensis cv. Valencia plants inoculated with Candidatus Liberibacter asiaticus. In a greenhouse of the Experimental Station-Autonomous University of Tamaulipas, the Candidatus Liberibacter asiaticus bacteria were inoculated to Citrus limon plants (growing on Citrus volkameriana, Citrus macrophylla, and Citrus aurantium rootstocks) and Citrus sinensis cv. Valencia (growing on Citrus volkameriana and Citrus aurantium rootstocks). The experiment was established under a completely randomized design with 45 graft/rootstock repetitions. In each graft/rootstock combination, the plant height and stem diameter were determined using a tape measurer and a Vernier, respectively. In addition, the nutrient content of foliar samples was determined by an X-ray fluorescence spectrometer. In both citrus species, the C. aurantium rootstock promoted a higher concentration of the bacteria. On the other hand, the rootstock that showed the best agronomical results after inoculation with the bacteria was C. volkameriana, presenting the least variation in mineral content and conferring greater plant height (15%) and stem diameter (23%). In contrast, the presence of Ca. Liberibacter asiaticus decreased S content and increased Cu concentration in C. lemon plants. Similarly, plants infected with C. sinensis presented higher Fe content. Finally, in both species, no significant differences were observed for Mn, P, and Zn concentration.