After teaching at the Colegio de Santo Tomas in Manila, he went to Japan in 1623, where he ministered incognito to the Catholic community for about ten years.

He worked as missionary to Pangasinan in the north of the island of Luzon and then at Binondo, a settlement for Chinese immigrants who had converted to Catholicism.

He worked incognito among the Christians for about ten years, comforting them, reconciling the apostates, and administering the sacraments in painfully difficult circumstances.

[3] Constantly sought by the authorities, he was denounced to government officials by a Christian apostate in July 1633 and interned in the prison of Nagoya.

[4] Ibáñez was aided in his missionary efforts by Francis Shoyemon, a Japanese layman who later was received into the Order of Preachers as a Dominican Cooperator Brother.