Pseudomonas aeruginosa (PA) is an opportunistic human pathogen and an etiological agent in cystic fibrosis (CF), leading to chronic infection and death. To understand how PA adapts to the harsh micro-environment of the CF host, we recently characterised three novel strains isolated from sputum of CF patients. We conducted genome sequencing, proteome profiling and phenotypic analysis and made comparisons to the laboratory strain PAO1. Genomic and phenotypic analyses revealed significant diversity in virulence, colonization and metabolism related traits in CF strains. 2D-LC-iTRAQ-MS analysis of carbonate-extracted membranes of all four strains of PA, grown in lung nutrient mimicking medium (SCFM) and M9 minimal medium revealed a total of 2,442 (SCFM) and 3,171 (M9) expressed proteins (global protein FDR <0.008%). Gene ontology and bioinformatics predictions assigned 994 (M9) and 765 (SCFM) proteins as membrane proteins. CF strains portrayed heterogeneity in membrane proteome expression which was reflected in phenotypes including biofilms, pigmentation, and virulence. We observed differential expression of key proteins involved in virulence, drug resistance, motility and adhesion. Interestingly, proteins involved in drug resistance (MexY, MexB, MexC, OprM) were up-regulated and chemotaxis, aerotaxsis (PA1561, PctA, PctB) motility and adhesion proteins (FliK, FlgE, FliD, PilJ) were downregulated in CF strains. Confirmatory phenotype assays including drug MIC, plate motility assay and sputum binding assay reinforced the observation by portraying increased antibiotic resistance and reduced motility and adhesion. In conclusion, our multi-omic analysis shows that the adaptation strategies of P. aeruginosa to CF lungs are both multifactorial and combinatorial and are tailored according to micro-environmental niches.