Huanglongbing (HLB) is the most threatening disease in global citriculture, causing significant economic losses in citrus groves worldwide. The disease is mainly associated with the bacterium Candidatus Liberibacter asiaticus (CLas). Current, HLB management involves the eradication of infected groves and the application of insecticides to control the psyllid vector. This study aims to understand the role of fatty acids in the pathogen-host interaction using a multi-omic approach. The dataset integrates lipidomics, proteomics, mass spectrometry imaging, SEM, FISH microscopy, and relative expression analyses. Access to the data is restricted for publication reasons. For further information, please contact the responsible authors.