Convoluted aero-engine intakes are often required to enable closer integration between engine and airframe. Although the majority of previous research focused on the distortion of S-duct intakes with undistorted inlet conditions, there is a need to investigate the impact of more challenging inlet conditions at which the intake duct is expected to operate. The impact of inlet vortices and total pressure profiles on the inherent unsteady flow distortion of an S-duct intake was assessed with stereo particle image velocimetry. Inlet vortices disrupted the characteristic flow switching mode but had a modest impact on the peak levels and unsteady fluctuations. Non-uniform inlet total pressure profiles increased the peak swirl intensity and its unsteadiness. The frequency of swirl angle fluctuations was sensitive to the azimuthal orientation of the non-uniform total pressure distribution. The modelling of peak distortion with the extreme value theory revealed that although for some inlet configurations the measured peak swirl intensity was similar, the growth rate of the peak values beyond the experimental observations was substantially different and it was related with the measured flow unsteadiness. This highlights the need of unsteady swirl distortion measurements and the use of statistical models to assess the time-invariant peak distortion levels. Overall, the work shows it is vital to include the effect of the inlet flow conditions as it substantially alters the characteristics of the complex intake flow distortion.