The coupling of the ionosphere to processes from below remains an elusive and difficult problem, as rapidly changing external drivers from above mask variations related to lower atmospheric sources. Here we use superposition of unique circumstances, current deep solar minimum and a record-breaking stratospheric warming event, to gain new insights into causes of ionospheric perturbations. We show large (50–150%) persistent variations in the low-latitude ionosphere (200–1000 km) that occur several days after a sudden warming event in the high-latitude winter stratosphere (∼30 km). We rule out solar irradiance and geomagnetic activity as explanations of the observed variation. Using a general circulation model, we interpret these observations in terms of large changes in atmospheric tides from their nonlinear interaction with planetary waves that are strengthened during sudden warmings. We anticipate that further understanding of the coupling processes with planetary waves, accentuated during the stratospheric sudden warming events, has the potential of enabling the forecast of low-latitude ionospheric weather up to several days in advance.