This work contributes to the understanding of mechanisms that lead to increased carbon monoxide (CO) concentrations in gas turbine combustion systems. Large-eddy simulations (LES) of a full scale high pressure prototype Siemens gas turbine combustor at three staged part load operating conditions are presented, demonstrating the ability to predict carbon monoxide pollutants from a complex technical system by investigating sources of incomplete CO oxidation. Analytically reduced chemistry is applied for the accurate pollutant prediction together with the dynamic thickened flame model. LES results show that carbon monoxide emissions at the probe location are predicted in good agreement with the available test data, indicating two operating points with moderate pollutant levels and one operating point with CO concentrations below 10 ppm. Large mixture inhomogeneities are identified in the combustion chamber for all operating points. The investigation of mixture formation indicates that fuel-rich mixtures mainly emerge from the pilot stage resulting in high equivalence ratio streaks that lead to large CO levels at the combustor outlet. Flame quenching due to flame-wall-interaction are found to be of no relevance for CO in the investigated combustion chamber. Post-processing with Lagrangian tracer particles shows that cold air—from effusion cooling or stages that are not being supplied with fuel—lead to significant flame quenching, as mixtures are shifted to leaner equivalence ratios and the oxidation of CO is inhibited.