Huanglongbing, or citrus greening disease, has devastated the citrus industry. It is associated with the gram negative bacterium Candidatus Liberibacter asiaticus (CLas) that can be transmitted by Diaphorina citri, the Asian citrus psyllid. For transmission to occur, CLas must cross the gut of the ACP to circulate through the insect body. The insect gut is the first site of widespread interactions between the CLas and the ACP and forms a barrier to transmission. To investigate the effect of CLas exposure on this dynamic interface, we performed RNAseq and mass spectrometry-based proteomics to analyze the transcriptome and proteome respectively of dissected ACP guts. We found changes in iron metabolism, insecticide resistance, immune system, and apoptosis. We identified 83 long non-coding RNAs that are responsive to CLas, two of which have no homology to other organisms in NCBI. We also determined that Wolbachia, a symbiont of the ACP, undergoes protein regulation when CLas is present. Fluorescent in situ hybridization (FISH) confirmed that Wolbachia and CLas can inhabit the same ACP gut cell, but do not co-localize. These data provide a snapshot of the ACP gut under normal and CLas-exposed conditions, and provide tools to better understand the insect vector of the citrus greening pathosystem.