Here he took an active part in the Chinese Rites controversy, between the Jesuits on the one side and the Dominicans and Franciscans on the other.
The latter maintained that the Jesuits, to make converts, tolerated to a certain extent the cult of Confucius and of ancestors.
They despatched Morales to Rome in 1643, and on 12 September 1645, obtained from Pope Innocent X a decision condemning the methods of the Jesuits.
About the same time the Dominicans discovered an enemy in their own ranks in the person of the Chinese friar, Luo Wenzao, Bishop of Basilea, who sent to the Holy See a memorandum favourable to the Jesuits.
While in Italy he recruited Vittorio Riccio, who would conduct extensive missionary work in Manila and south-east China.