In recent years, the conflict generated between Catalonia and Spain has produced cases in which, due to the political tensions, recognized citizens announced a change of domicile: from the rest of Spain to Catalonia, from Catalonia to the rest of Spain or abroad. This is an observed pattern at media and “popular” levels, but there is no scientific study devoted to this. The phenomenon represents an ideal case for studying how citizenship moves to other jurisdictions when their preferences and their expectations do not match the policies of the place where they reside. The paper explores the effect of the independence process in Catalonia, namely changes in territorial preferences and political polarization, on the mobility of Catalan and Spanish citizens at municipality level. This analysis is to be done by processing aggregated data from the municipal board at the level of census sections. Using this data, we extract the internal migratory fluxes and estimate their political causes through the use of several variables as control factors. Our contribution allows for a better understanding of territorial conflicts using a new dataset. Further research can rely on our contribution and data to explore the impact of conflicts on mobility patterns of population across jurisdictions.