Little more than a year after, fresh trouble arose with the king, and Anselm resolved to proceed to Rome and seek the counsel of his spiritual father. With great difficulty he obtained a reluctant permission to leave, and in October 1097 he set out for Rome. William immediately seized on the revenues of the see, and retained them to his death. Anselm was received with high honour by Urban, and at a great council held at Bari, he was put forward to defend the doctrine of the procession of the Holy Ghost against the representatives of the Greek Church. But Urban was too politic to embroil himself with the king of England, and Anselm found that he could obtain no substantial result. He withdrew from Rome, and spent some time at the little village of Schiavi, where he finished his treatise on the atonement, _Cur Deus homo_, and then retired to Lyons.
In 1100 William was killed, and Henry, his successor, at once recalled Anselm. But Henry demanded that he should again receive from him in person investiture in his office of archbishop, thus making the dignity entirely dependent on the royal authority. Now, the papal rule in the matter was plain; all homage and lay investiture were strictly prohibited. Anselm represented this to the king; but Henry would not relinquish a privilege possessed by his predecessors, and proposed that the matter should be laid before the Holy See. The answer of the pope reaffirmed the law as to investiture. A second embassy was sent, with a similar result. Henry, however, remained firm, and at last, in 1103, Anselm and an envoy from the king set out for Rome. The pope, Paschal, reaffirmed strongly the rule of investiture, and passed sentence of excommunication against all who had infringed the law, except Henry. Practically this left matters as they were, and Anselm, who had received a message forbidding him to return to England unless on the king's terms, withdrew to Lyons, where he waited to see if Paschal would not take stronger measures. At last, in 1105, he resolved himself to excommunicate Henry. His intention was made known to the king through his sister, and it seriously alarmed him, for it was a critical period in his affairs. A meeting was arranged, and a reconciliation between them effected. In 1106 Anselm crossed to England, with power from the pope to remove the sentence of excommunication from the illegally invested churchmen. In 1107 the long dispute as to investiture was finally ended by the king resigning his formal rights. The remaining two years of Anselm's life were spent in the duties of his archbishopric. He died on the 21st of April 1109. He was canonized in 1494 by Alexander VI.