By a pontifical letter of Paul III, dated January 1, 1547, and renewed by Julius III in 1552 he had been appointed governor and architect of St. Peter's with full power to carry on the construction. He accepted this heavy task as a sacred duty, and refused to take any pay for it. In 1557 he wrote to his nephew Lionardo, "many people believe, as I do myself, that I have been placed at this post by God. I will not leave it because I am serving for the love of God and put all my hope in Him."[86]
He at once found himself in trouble with the party of San Gallo. They had always been his enemies and it must be acknowledged that he had done his best to deserve their hostility.
When Raphael was directing the work on St. Peter's, Antonio da San Gallo had been his assistant, and he therefore belonged to the party opposed to Michelangelo. In 1537 San Gallo became architect-in-chief, succeeding Baldassare Peruzzi, and he abandoned, as Raphael had done, Bramante's great design for the main construction. Michelangelo, on the contrary, went back to that plan, for whatever rancour he might feel against Bramante personally, his genius bowed before that of the great architect. He wrote in 1555 to Bartolommeo Ammanati, "It can not be denied that in architecture Bramante was greater than any other man since classic times. He conceived the first design for St. Peter's, simple, clear and free from all confusion, and whoever like San Gallo has turned aside from this plan has turned aside from the truth."
Before the disagreement over St. Peter's, Michelangelo had twice come into sharp conflict with San Gallo over the fortifications of the Borgo and the completion of the Farnese palace.
Paul III wished to reconstruct and complete the fortifications of Rome which had been destroyed in 1527. San Gallo had been engaged on them since 1534, but the work had only been actively pushed since 1542. In February, 1545, meetings were held under the presidency of Pier Luigi Farnese in the Castle of St. Angelo to discuss the subject of the fortifications of the Borgo, and to these Michelangelo was summoned. He expressed opinions absolutely opposed to those of San Gallo and enumerated the faults already committed in the works. Hot words were exchanged, and the pope was obliged to command both men to be silent. Soon after this affair Michelangelo made a new design for the fortifications involving the destruction of San Gallo's work, and this was accepted.[87]