Context. The 30-year recurrent symbiotic nova V3890 Sgr exploded 2019 August 28 and was observed with multiple X-ray telescopes. Swift and AstroSat monitoring revealed slowly declining hard X-ray emission from shocks between the nova ejecta and the stellar wind of the companion. Later, highly variable Super-Soft-Source (SSS) emission was seen. An XMM-Newton ⋆ observation during the SSS phase captured the high degree of X-ray variability in terms of a deep dip in the middle of the observation. Aims. This observation adds to the growing sample of diverse SSS spectra and allows spectral comparison of low-and high-state emission to identify the origin of variations and subsequent effects of such dips, all leading to new insights into how the nova ejecta evolve. Methods. Based on initial visual inspection, quantitative modelling approaches were conceptualised to test hypotheses of interpretation. The light curve is analysed with a power spectrum analysis before and after the dip and an eclipse model to test the hypothesis of occulting clumps like in U Sco. A phenomenological spectral model (SPEX) is used to fit the complex RGS spectrum accounting for all known atomic physics. A blackbody source function is assumed like in all atmosphere radiation transport models while the complex radiation transport processes are not modelled. Instead, one or multiple absorbing layers are used to model the absorption lines and edges, taking into account all state of the art knowledge of atomic physics. Results. In addition to the central deep dip, there is an initial rise of similar depth and shape and, after the deep dip, there are smaller dips of ∼ 10% amplitude, which might be periodic over 18.1-minutes. Our eclipse model of the dips yields clump sizes and orbital radii of 0.5-8 and 5-150 white dwarf radii, respectively. The simultaneous XMM-Newton UV light curve shows no significant variations beyond slow fading. The RGS spectrum contains both residual shock emission at short wavelengths and the SSS emission at longer wavelengths. The shock temperature has clearly decreased compared to an earlier Chandra observation (day 6). The dip spectrum is dominated by emission lines like in U Sco. The intensity of underlying blackbody-like emission is much lower with the blackbody normalisation yielding a similar radius as during the brighter phases, while the lower bolometric luminosity is ascribed to lower T eff . This would be inconsistent with clump occultations unless Compton scattering of the continuum emission reduces the photon energies to mimic a lower effective temperature. However, systematic uncertainties are high. The absorption lines in the bright SSS spectrum are blue-shifted by 870 ± 10 km s −1 before the dip and slightly faster, 900 ± 10 km s −1 , after the dip. The reproduction of the observed spectrum is astonishing, especially that only a single absorbing layer is necessary while three such layers are needed to reproduce the RGS spectrum of V2491 Cyg. The ejecta of V3890 Sgr are thus more homogeneous than many other SSS ...