In matters of doctrine the pope supported Bernard of Clairvaux in his prosecution of Abelard and Arnold of Brescia, whom he condemned as heretics.
His apologists explain that his action was merely "official," but Bonner was one of those who brought it to pass that the condemnation of heretics to the fire should be part of his ordinary official duties.
Among the principal events of that reign must be reckoned the foundation of the two orders, Franciscan and Dominican, who were destined to form a militia for the holy see in conflict with the empire and the heretics of Lombardy.
He saw Jews, Saracens, heretics and apostates roaming through Spain unmolested; and in this lax toleration of religious differences he thought he saw the main obstacle to the political union of the Spains, which was the necessity of the hour.
In the next year he ceded to Diego Deza, a Dominican, his office of confessor to the sovereigns, and gave himself up to the congenial work of reducing heretics.