The Emperor bemoaned "the loss that we have made and principally I who held her as a mother and for the lack she does me in the government of the countries where she was in charge." Margaret's will appointed Charles as her sole heir and urged her nephew to protect the sovereignty of the Low Countries against the centralizing tendency of his imperial administrators. She was buried alongside her second husband at Bourg-en-Bresse, in the mausoleum of the Royal Monastery of Brou that she previously commissioned. There is a statue of the Governess next to the Cathedral of Mechelen.