1139–1146: Rainier, died 28 February 1146, abbot before the first group of monks arrives in 1149.
1146–1147: Bertolde, from Cologne.
1147–1155: Osbert, abbot for 8 years, retired in 1155.
1163 Milon de Trainel, abbot of Saint Marien, asked King Louis VII to fortify the abbey in exchange for land to preserve the religious "Vaul Parfunde" against incursions of all kinds. He rebuilt St. Marien next to the Church of St. Martin.
1209–1222: Norbert, elected in 1209. Norbert is mentioned in the 67th letter of Gervais, which discusses that St. Marien is in debt and some wish to not build a dining hall.
1223: Rainier II attends a judgment in Saint-Fargeau against the Count de Mello in favor of the cathedral
1239: Hulderus is mentioned in a charter of Gautier, regarding the agreement between the inhabitants of Bassou and their priest
1246: Guillaume sells a tenement of Auxerre
Étienne, also an abbot of Saint-Paul
before 1264–1269: Guerric, Burgundinian by birth, elected in 1269. Known for his world chronicle which recorded history as far back as 1190 and was later published in 1608.
before 1281 – after 1288: Jean attends the tribute of the Count of Flanders in 1281.
1291 – Unknown : Henri
1302: Martin Blake is appointed in arbitration proceedings for Chapter Auxerre
before 1358 – after 1360: EtienneII acknowledges the abbey's debt to the monks of Saint-Germain, who paid the ransom demanded by the English at Auxerre.
before 1364 – after 1380: Jean II compromises in 1364 with Étienne de Chitry, Abbé de Saint-Germain.
1402–1419: Richard Colas, previously pastor of Notre-Dame-La-D'Hors. Elected ecclesiastical governor of City Hall in 1411 and 1412. His grave was found in 1715 in the Church of the Notre-Dame-La-D'Hors and brought to St. Martin.
Unknown – 1456: Pierre Aulard was excommunicated in 1423 by the bishop of Auxerre Philippe Dessessart for failing to attend the synod of 1423; he is absolved ad cautelam a few years later by the Abbot of St. Genevieve, curator of the privileges of the order of Norbertine.
1457–1479: Jean Veraudat, born in Appoigny. Ecclesiastical governor of the town hall in 1477 and 1478.
1479–1496: Jean Bourgeois, elected abbot on 31 August 1479. Jean Baillet was the bishop at the time, and blessed him in Paris during October 1479. In 1485, he formed the Council of Sens. In 1496, he chose a co-Adjuteur and died six days later.
1496 - c.1540: Nicolas Sacra, from an old family of Auxerre, was chosen as co-Adjuteur of Father John. Focused on order, he reformed a large number of houses as the General Chapter in 1498 and the Abbot of Prémontré in 1511. Ecclesiastical governor of the City Hall in 1518.
c.1540 - c.1552: Arnoul Gonthier
c.1552 – 1561: Pierre Fournier, a noble of Auvergne, became bishop of Périgueux in 1561.
c.1564 - c.1567: Michel de Clugny
Unknown – 1579: François Guerry
1579–1583: Jean Lourdereaux
1583–1598: Jean Lourdereaux, brother of the previous abbot.
1598–1627: Edme Martin
1628–1639: Nicolas de Castille, son of Pierre de Castille
1639–1670 or 1671: Henri de Castille, son of Pierre de Castille
