One of the biggest challenges to quality of life for an individual with Cystic Fibrosis (CF) is the high rate of incidence of infection with the frequent isolate Pseudomonas aeruginosa. Infections are typically lifelong, resulting in significant morbidity and mortality, and lead to high rates of divergent within-host evolution, often resulting in the presence of multiple infection phenotypes. This renders traditional therapies / interventions ineffective. We profiled within-host adaptation by investigating a pair of isogenic clonal epidemic isolates (AES-1R and AES-1M), isolated from the same patient 11 years apart. Using a combined -omic strategy, isolates were grown in an artificial sputum-like medium that reflects the physiology of the CF lung. We undertook intra- and extra-cellular comparisons at the proteomics level using offline HILIC peptide fractionation coupled to reversed phase LC-MS/MS, which enabled the identification of functional clusters associated with virulence that were highly expressed only in the initial colonizing isolate. Proteome data was integrated with metabolome and lipidome data extracted from the same cells, using a targeted (MRM) and untargeted mass spectrometric method, respectively. Integration of multiple -omics revealed distinct metabolic preferences between the two strains that reflects niche adaptation. Differences in virulence capabilities were assessed through confocal scanning laser microscopy to investigate changes in biofilm structure, cell membrane glycolipid analysis by MALDI-TOF MS, as well as virulence in the classical C. elegans slow-killing and murine lung-infection models. Host-pathogen interactions were investigated using 16-colour flow cytometry within the murine lung, in tandem with qPCR to quantify in vivo virulence network expression. The results obtained provide one of the most comprehensive assessments to date of the consequences of over a decade of within-host evolution on the cellular physiology of P. aeruginosa in adaptation and persistence within the context of CF.