Rootstocks are a key component of commercial citrus production. Therefore, rootstock improvement is a major breeding objective of citrus breeding programs. Improved citrus rootstocks are a potential solution to combat Huanglongbing (HLB), a bacterial disease which is caused by putative causal agent CaLas. The citrus breeding program at the University of Florida, Citrus Research and Education Center (UF-CREC) has developed many putative HLB-tolerant rootstocks that can enhance 'Valencia' sweet orange scion sustainability and fruit quality under endemic HLB condition. Differential transcriptomic analysis of HLB -asymptomatic and -symptomatic 'Valencia' (VAL) scion grafted onto UF-CREC improved candidate (CAN) rootstock (a putatively HLB tolerant rootstock, hybrid of Hirado Buntan pummelo and Cleopatra mandarin) and commercially used Swingle (SW) rootstock, showed significant differential expression regulation of transcripts involved in the jasmonic acid (JA), ethylene (ET), abscisic acid (ABA), auxin (AU) and brassinosteroid (BR) hormonal metabolism. In asymptomatic (leaves) and symptomatic (leaves and roots) VAL/SW leaves showed significant upregulation of genes encoding in ABA response regulation, AU biosynthesis, and ET biosynthesis and receptors as compared to the respective treatments of VAL/CAN indicating possible activation of response to abiotic stress, and strong involvement of AU and ET mediated responses in CaLas-infected VAL/SW. In VAL/CAN, significant upregulation of AU response factors and BR response genes suggests that the enhanced plant sustainability might be the outcome of AU-BR interactions. VAL/SW also showed upregulation of different JA biosynthesis genes suggesting a defense activation, possibly against the psyllid phloem feeding. The transcriptome comparison results also showed a greater number of defense-associated genes upregulated in leaves and roots of VAL/SW combination which seem to exhibit a high energy requirement condition that compromises plant growth. Therefore, strong upregulation of defense genes in VAL/SW seems to be a reason for poor plant health in the advanced stage of CaLas-infection. Whereas significant upregulation of nutrient transporters, cell wall modification genes, phloem regeneration associated genes, growth factors and AUBR interactions suggest a better energy distribution balance between defense and growth in VAL/CAN plants. In a greenhouse study, VAL grafted onto a UF-CREC created improved complex tetraploid (4x) rootstock and SW showed significant differences in the plant phenotype and nutrient transporter genes expression. Ca Las-infected-VAL/4x plants had a superior phenotype and lower HLB bacterial titer as compared to VAL/SW under traditional and enhanced controlled release fertilizer (ECRF). Also, CaLas infected -VAL/SW phenotype improved under ECRF. Our findings in the field and greenhouse experiments support the hypothesis that rootstock can differentially reprogram CaLas-infected scion to improve plant performance. Moreover, there appears to be a significant rootstock-nutrition interaction that plays a role in the defense response.