Rain-on-snow (ROS) events have caused severe floods inmountainous areas in the recent past. Because of the complex interactions of physical processes, it is still difficult to accurately predict the effect of snow cover on runoff formation for an upcoming ROS event. In this study, a detailed physics-based energy balance snow cover model (SNOWPACK) was used to assess snow cover processes duringmore than 1000 historical ROS events at 116 locations in the Swiss Alps. The simulations of the mass and energy balance, liquid water flow, and the temporal evolution of structural properties of the snowpack were used to analyze runoff formation characteristics during ROS events. Initial liquid water content and snow depth at the onset of rainfall were found to influence the temporal dynamics, intensities, and cumulative amount of runoff. The meteorological forcing is modulated by processes within the snowpack, leading to an attenuation of runoff intensities for intense and short rain events and an amplifying effect for longer rain events. The timing of runoff generation relative to the rainfall seems to be strongly dependent on initial liquid water content, snow depth, and rainfall intensities. As these snowpack and meteorological conditions usually exhibit a strong seasonality, cumulative runoff generation during ROS also varies seasonally. ROS events with intensified snowpack runoff were found to be most common during late snowmelt season, with several such events also occurring in late autumn. These results demonstrate the strong influence of initial snowpack properties on runoff formation during ROS events in the Swiss Alps.