We present results from the spectral analysis of a long XMM-Newton observation of the radio-loud NLS1 galaxy PKS0558-504. The source is highly variable, on all sampled time scales. We did not observe any absorption features in either the soft or hard X-ray band. We found weak evidence for the presence of an iron line at ~6.8 keV, which is indicative of emission from highly ionized iron. The 2-10 keV band spectrum is well fitted by a simple power law model, whose slope steepens with increasing flux, similar to what is observed in other Seyferts as well. The soft excess is variable both in flux and shape, and it can be well described by a low-temperature Comptonisation model, whose slope flattens with increasing flux. The soft excess flux variations are moderately correlated with the hard band variations, and we found weak evidence that they are leading them by ~20 ksec. Our results rule out a jet origin for the bulk of the X-ray emission in this object. The observed hard band spectral variations suggest intrinsic continuum slope variations, caused by changes in the heating/cooling ratio of the hot corona. The low-temperature Comptonising medium, responsible for the soft excess emission, could be a hot layer in the inner disc of the source, which appears due to the fact that the source is accreting at a super-Eddington rate. The soft excess flux and spectral variations could be caused by random variations of the accretion rate.