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Increasing differences with the convent led to his resignation in 1506, when he decided to take up the offer of the Bishop of Würzburg, Lorenz von Bibra (bishop from 1495 to 1519), to become the abbot of St. James's Abbey, the Schottenkloster in Würzburg.
Wilhelm was a member of the aristocratic Franconian von Bibra family which among its members were Wilhelm’s half brother, Lorenz von Bibra Prince-Bishop of Würzburg, Duke in Franconia, Conrad von Bibra, Prince-Bishop of Würzburg, Duke in Franconia (1490-1544), Heinrich von Bibra, Prince-Bishop, Prince-Abbot of Fulda (1711-1788) and Ernst von Bibra (1806-1878), naturalist and author.