Pseudomonas aeruginosa is known as opportunistic pathogen frequently isolated from different infection sites such as burned wounds, lung and urinary tract. To shed light on the expression rates of cytoplasmic P. aeruginosa proteins, commonly expressed by eleven different clinical isolates, absolute protein quantities were determined using P. aeruginosa PAO1 as a reference strain and employing a highly precise gel-free and data-independent LC-IMSE approach. Moreover, the metabolic diversity of these isolates has been investigated by 13C-metabolic flux analyses. 903 proteins were reproducibly identified and absolutely quantified for P. aeruginosa PAO1, 363 of which were also identified and relatively quantified in all of the tested clinical isolates. The vast majority of these proteins is expressed in constant amounts in all strains and exhibits a relatively low relative standard deviation. In contrast, the expression rates of 42 proteins were highly variable between the isolates. Notably, the outer membrane protein OprH and the response regulator PhoP were strongly expressed in isolates from burned wounds when compared to isolates from lung or urinary tract. Moreover, proteins involved in the uptake of iron and amino acids (i.e. HitA, BfrB, PA5217, BraC, PA5153) were found to be more abundant in urinary tract isolates compared to lung isolates. The fluxome data revealed a conserved glycolysis, and a niche-specific divergence in fluxes through the glyoxylate shunt and the TCA cycle among the isolates. The integrated analysis of proteome and fluxome did not indicate straightforward correlation between the amount of proteins and their flux, but rather points to additional layers of regulation that mediate metabolic adaption of P. aeruginosa to different host environments.