The disastrous earthquake of 1693 AD caused over 60,000 causalities and the total destruction of several villages and towns in south-eastern Sicily. Immediately after the earthquake, a tsunami struck the Ionian coasts of Sicily and the Messina Strait and was probably recorded even in the Aeolian Islands and Malta. Over the last few decades, the event has been much debated regarding the location of the seismogenic source and the possible cause of the associated tsunami. The marine event has been related to both a submarine landslide and a coseismic displacement at the seafloor. To better define the most reliable sources and dynamics of the tsunami, we couple high-resolution marine seismic survey data with hydrodynamic modelling to simulate various scenarios of tsunami generation and propagation. Results from the simulations are compared with geomorphological evidence of past tsunami impacts, described in previous work along the coast of south-eastern Sicily, and within historical chronicles and reports. The most reliable scenario considers the 1693 event composed by two different tsunami waves: a first wave generated by the coseismic fault displacement at the seafloor and a second wave generated by a submarine landslide, triggered by the earthquake shaking. Tsunami modelling shows that a simultaneous movement between fault displacement and submarine mass movement could determine a destructive interference on the tsunami waves, resulting in a reduction in wave height. For this reason, the second tsunami wave probably occurred with a maximum delay of few minutes after the one generated by the earthquake and induced a greater flooding. The double-source model could explain the observation because in the course of other destructive earthquakes in south-eastern Sicily, such as that of 1169 AD, the associated tsunami caused less damages. This implies the need to better map, define and assess the hazard responsible for this type of tsunami events.