Charles was greatly distressed when he learned that his beloved aunt had passed away, and ordered magnificent obsequies to be performed in the cathedral of Cologne, which he attended with his whole Court. The funeral sermon, delivered in Latin by Jean Fabri, was listened to with rapt attention by the large congregation which filled the building.
Margaret was deeply mourned by all who knew her, and especially by the people over whom she had ruled so well.
In her will she directed that her heart should be given to the Convent of the 'Annonciades' at Bruges, her intestines to the church of St. Peter and St. Paul at Malines, and her body to the Monastery of St. Nicolas de Tolentin at Bourg en Bresse, where she wished to be buried beside her husband, Philibert of Savoy, in the church of Brou.
Her funeral services began in the church of St. Peter and St. Paul at Malines by three solemn masses, and were continued in the cathedral church of St. Rombault, which was hung with 120 yards of black cloth for the occasion. The Archbishop of Palermo conducted the service, which was attended by the Grand Council and Magistrates, and all the guilds of the city. Here Cornelius Agrippa preached her funeral oration, dwelling at much length on her many virtues and great talents. 'We have lost,' he said, 'the anchor on which our hopes rested. We are weighed down with this great affliction, for no greater loss could have befallen us and our country. What consolation can we find in the death of the very saintly Princess Margaret? We all weep, we all lament her! All the provinces, all the cities, all the towns, all the villages, all the hamlets are plunged in grief, sorrow, and mourning.'
On the 22nd of January 1531, a funeral procession, headed by the young Crown Prince of Denmark, as chief mourner, escorted Margaret's body and heart to Bruges. Whilst awaiting translation to its final resting-place at Brou, her body was laid in a vault beneath the high altar in the Convent of the 'Annonciades'; her heart, enclosed in an urn, was placed in the tomb of her mother, Mary of Burgundy, in the church of Notre-Dame, but on the 6th of February following, it was given to the Mère Ancille by the emperor's command to replace her body, which, on April the 21st, 1532, was sent to Brou. This long delay in carrying Margaret to her final resting-place was due to the fact that at the time of her death the church of Brou was not finished, and it was two years before the tombs were completed. But at last in June 1532 Margaret was laid to rest beside Philibert and his mother in the beautiful church which her love and piety had called into being, but whose glories she had not lived to see completed. The funeral ceremonies lasted three days, the 10th, 11th, and 12th of June. Accompanied by the chief men of the town, the Syndic of Bourg went out to meet the funeral cortège, which was escorted by the Marshal of Burgundy, the Count of Hochstrate, the Archdeacon of Fauverny, and Claud de Boisset, who was afterwards Bishop of Arras. At the service the sermon was preached by Brother Anthony of Saix, Commander of the Abbey of St. Anthony of Bourg, in French as well as in Latin, so that all might understand. Amongst her many talents he mentioned 'her subtle excellence in painting,' in which pastime he asserted she frequently indulged.
The leaden urn which contained her intestines was placed in a vault in front of the high altar in the church of St. Peter and St. Paul at Malines, but in 1778 the urn was found to be much damaged, and was enclosed in an oaken chest, and reburied under one of the stone slabs in the choir, between the first step of the high altar and the wall, where a small X in the pavement marks the spot.
By her will Margaret dowered fifty maidens of Bresse with fifty pounds apiece, and amongst other legacies bequeathed her wine-glass incrusted with silver, a silver spoon and silver medal to the 'Annonciades' at Bruges; besides a gilded and illuminated copy of the Gospel of St. John, and her rosary, which contained ten agates, on the largest of which were engraved the virtues of the Holy Virgin Mary. This relic had been worn by Jeanne de Valois, the unhappy wife of Louis XII. of France, foundress of the Order of the Annunciation. The other stones were interspersed with small beads of gold, a gold heart hanging from the end of the rosary. This gift was accompanied by a portrait of Margaret painted on wood by Bernard van Orley, and two touching letters addressed to the Mère Ancille. The Church of the 'Annonciades' was demolished in 1578, when the nuns retired to a house called 'Fluweelhof' at Bruges, carrying Margaret's remains with them.
In 1531 the emperor caused an alabaster monument, decorated with gold statuettes, to be erected to Margaret's memory in the church outside the Porte des Anes. But in 1578 it was horribly mutilated by the rebels, and what was left of it was transferred in 1714 to the church of the new Convent at Fluweelhof. A pavement of black and white marble was added, and a figure representing the Annunciation of the Virgin, before whom Margaret was depicted kneeling at her prie-dieu, holding her 'Book of Hours' in her hands, with her patron saint, Margaret, behind her, and her maids of honour by her side, bearing the arms of the empire, Burgundy, Bourbon, and Castile. The débris of the former monument was used to make these figures. In the centre of the niche containing the monument was placed a painted heart in a mirror with this inscription in Flemish:—
'Here lies the noble heart of the very excellent Archduchess of Austria, Madame Margaret, daughter of the invincible Emperor Maximilian and of the Lady Mary of Burgundy, his wife, foundress of this Convent of the Annunciation at Bruges, niece of Jeanne, Queen of France, and foundress of the Order of the Annunciation, widow of the Prince of Spain, etc., aunt of his Imperial Majesty Charles V., who gave this heart in the year 1531, the 6th of Feb., in eternal remembrance.'
In the same niche behind the figure of St. Margaret is the inscription which the emperor also caused to be erected at Malines:—