jats:pThe large-scale coherent motions in a realistic swirl fuel-injector geometry are analysed by direct numerical simulations (DNS), proper orthogonal decomposition (POD), and linear global modes. The aim is to identify the origin of instability in this turbulent flow in a complex internal geometry. The flow field in the nonlinear simulation is highly turbulent, but with a distinguishable coherent structure: the precessing vortex core (a spiralling mode). The most energetic POD mode pair is identified as the precessing vortex core. By analysing the fast Fourier transform (FFT) of the time coefficients of the POD modes, we conclude that the first four POD modes contain the coherent fluctuations. The remaining POD modes (incoherent fluctuations) are used to form a turbulent viscosity field, using the Newtonian eddy model. The turbulence sets in from convective shear layer instabilities even before the nonlinear flow reaches the other end of the domain, indicating that equilibrium solutions of the Navier–Stokes are never observed. Linear global modes are computed around the mean flow from DNS, applying the turbulent viscosity extracted from POD modes. A slightly stable discrete jats:inline-formulajats:alternatives<jats:inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" mime-subtype="gif" xlink:type="simple" xlink:href="S0022112016000860_inline1" />jats:tex-math$m=1$</jats:tex-math></jats:alternatives></jats:inline-formula> eigenmode is found, well separated from the continuous spectrum, in very good agreement with the POD mode shape and frequency. The structural sensitivity of the precessing vortex core is located upstream of the central recirculation zone, identifying it as a spiral vortex breakdown instability in the nozzle. Furthermore, the structural sensitivity indicates that the dominant instability mechanism is the Kelvin–Helmholtz instability at the inflection point forming near vortex breakdown. Adjoint modes are strong in the shear layer along the whole extent of the nozzle, showing that the optimal initial condition for the global mode is localized in the shear layer. We analyse the qualitative influence of turbulent dissipation in the stability problem (eddy viscosity) on the eigenmodes by comparing them to eigenmodes computed without eddy viscosity. The results show that the eddy viscosity improves the complex frequency and shape of global modes around the fuel-injector mean flow, while a qualitative wavemaker position can be obtained with or without turbulent dissipation, in agreement with previous studies. This study shows how sensitivity analysis can identify which parts of the flow in a complex geometry need to be altered in order to change its hydrodynamic stability characteristics.</jats:p>