In this study, we examine marine low cloud cover variability in the Southeast Pacific and its association with lower-tropospheric stability (LTS) across a spectrum of timescales. On both daily and interannual timescales, LTS and low cloud amount are very well correlated in austral summer (DJF). Meanwhile in winter (JJA), when ambient LTS increases, the LTS–low cloud relationship substantially weakens. The DJF LTS–low cloud relationship also weakens in years with unusually large ambient LTS values. These are generally strong El Niño years, in which DJF LTS values are comparable to those typically found in JJA. Thus the LTS–low cloud relationship is strongly modulated by the seasonal cycle and the ENSO phenomenon. We also investigate the origin of LTS anomalies closely associated with low cloud variability during austral summer. We find that the ocean and atmosphere are independently involved in generating anomalies in LTS and hence variability in the Southeast Pacific low cloud deck. This highlights the importance of the physical (as opposed to chemical) component of the climate system in generating internal variability in low cloud cover. It also illustrates the coupled nature of the climate system in this region, and raises the possibility of cloud feedbacks related to LTS. We conclude by addressing the implications of the LTS–low cloud relationship in the Southeast Pacific for low cloud feedbacks in anthropogenic climate change.