Aspergillus fumigatus is an environmental saprophyte and an opportunistic pathogen of the human airway. A. fumigatus can cause chronic infections, typically in the context of preexisting lung damage or disease, colonising dead or dying tissue. Animal models of this condition are costly and often cannot reflect an accurate phenotype observed in patients. The ex-vivo pig lung model (EVPL) was developed for conducting bacterial infection studies as pigs share a 90% immunological homology to humans and in addition to share many anatomical similarities. EVPL retains resident immune cells and richer cell type complexity compared to organoid models, in addition to a microbiome. We have adapted this model to study chronic pulmonary aspergillosis. Proteomic analysis enabled tracking of molecular changes to the pathogen and the host during the initial establishment of fungal infection. Results revealed increased abundance of proteins identified associated with carbohydrate metabolism at 48 hours and protein metabolism at 72 and 96 hours. Importantly proteins associated with amino acid metabolic, and biosynthesis processes were detected prior to the detection of fungal toxin biosynthesis. This supports clinical findings that amino acid biosynthesis is an important process in fungal virulence as it may fuel the production of many toxic metabolites. This similarity in response validates the use of the model and contributes supporting evidence that this process is of clinical importance during early-stage fungal colonisation and establishment of infection.