The use of Biological Control Agents (BCAs) to cope diseases has received considerable attention owing to its high efficiency and environmental safety. The aim of our study was to investigate the potential role of the Pseudomonas mediterranea pre-treatments in the response of lemon [Citrus limon (L.) Burm. f.] against mal secco, this being a devastating citrus disease caused by the fungus Plenodomus tracheiphilus. RNAseq analysis revealed that the fungus induced a marked reprogramming of the transcriptome, but P. Mediterranea pre-treatments strongly reduced lemon leaf transcriptome modifications and limited the amount of the fungus DNA inside the plant tissue. Furthermore, P. mediterranea prevented the down regulation of the genes involved in the effector triggered immunity (ETI) and the deregulation of genes involved in the main phytohormone’s biosynthesis and perception. As far as we know, this work represents the first report on the analysis of P. tracheiphilus-lemon plant-BCA interaction at molecular level. Overall design: Potted lemon 'Femminello Siracusano 2Kr' plants grafted onto Citrus aurantium (sour orange) kept in greenhouses at Agrobiotech srl (Catania) were used for the inoculation tests. The inoculations with the fungal pathogen were carried out by placing 10 µl of the vial suspension of P. tracheiphilus isolated PVCT Pt57 (see paragraph 2.2) on the secondary veins of young but fully expanded leaves; the droplets were then pierced until the leaf was incised with an awl with three entomological needles mounted at the end (Oliveri et al., 2022). Each leaf was inoculated in four spots. In order to evaluate the effect of the treatment with the biocontrol agent, the following theses were defined as follows: 3C thesis, plants treated with the biocontrol agent three days and one day before H2O inoculation; 3CPt thesis, plants treated with the biocontrol agent three days and one day before P. tracheiphilus inoculation; Pt thesis: plants treated with water three days and one day before P. tracheiphilus inoculation; CK thesis, plants treated and inoculated with dH2O. Six plants were inoculated for each thesis and, in each of these, three branches and at least six leaves per branch, for a total of about 18 leaves per plant. The leaves intended for transcriptomic analysis were collected 7 days after inoculation before symptom appearance.