The pea aphid, Acyrthosiphon pisum, requires the nutritional endosymbiont, Buchnera, for the production of essential amino acids. However, it is unclear if host plant diet that varies in essential amino acids influences aphid regulation of its nutritional symbioses. We hypothesized that aphid genes respond to host plant diet when aphids feed on their specialized (alfalfa) compared to universal host plant diet (fava), which vary in essential amino acid concentrations. Using RNA-Seq and whole genome bisulfite sequencing, we compared the gene expression profiles and DNA methylation distributions of specialized aphid cells that harbor Buchnera (bacteriocytes) when aphids feed on their specialized compared to their universal host plant diets. Our results show that bacteriocyte transcription and methylation patterns differ between host plant diets. When aphids feed on their specialized host plant, they significantly up-regulate and/or hypo-methylate key aphid genes in bacteriocytes related to the amino acid metabolism, including glutamine synthetase (GS) and the glutamine transporter ApGLNT1. Moreover, regardless of which host plant aphids feed on, we observed significant up-regulation and differential methylation of the key genes in the amino acid metabolism and the glycine/serine metabolism in aphid bacteriocytes. We suggest that the regulatory response of key symbiosis genes in bacteriocytes allows aphids to feed on a specialized host plant diet with suboptimal nitrogen concentrations.