The special issue "Vertical coupling in the atmosphere–ionosphere system" invites papers dealing with the investigation of the coupling phenomena in the neutral atmosphere–ionosphere system. It covers processes in the atmosphere–ionosphere system that significantly influence and/or govern the coupling within the regions. The coupling effects can be seen in the modulation of the waves from the lower to upper atmosphere as well as from low to high latitudes, electrodynamic and compositional changes, and plasma irregularities at different latitudinal regions around the globe due to the varying energy inputs. Solar activity represents an important factor that directly or indirectly modulates the coupling processes. The core of the special issue will be formed by the recent results presented during the 7th IAGA/ICMA/SCOSTEP Workshop on the Vertical Coupling in the Neutral Atmosphere-Ionosphere System held in Potsdam, Germany, in July 2018, and the special issue is open to further contributed papers as well. Topics include (1) ionospheric and thermospheric variability induced by the propagation, breaking, and modulation of atmospheric tides and planetary waves, (2) middle atmospheric effects of planetary waves, as well as their interannual variability, (3) ionospheric variations due to varying energy inputs from the Sun and from the lower atmosphere, (4) effects of solar eclipses, tropospheric storms and lightning, (5) chemical and dynamical changes observed in the MLT, and (6) upper atmospheric changes caused by increasing carbon dioxide concentrations and tropospheric climatological effects such as ENSO. Manuscripts on theoretical, modelling, and observation-based studies are solicited.