After being Secretary of State, the Congregation was considered an important though lesser assignment. The Pope did not appoint him as Prefect, because at the time the Popes themselves were Prefects of the Holy Office. The post of Secretary was then the highest-ranking office in the Dicastery. Merry del Val as secretary was responsible for running the daily affairs of the Holy Office, in which capacity he reportedly explained Pope Pius's policy of non possumus to Theodore Herzl and his emerging movement of Zionism, saying that as long as Jews deny Christ's divinity, the Church could not make a declaration in their favor. When the British Catholic diplomat Mark Sykes visited him to speak about the same topic, Merry del Val was more supportive, indicating that the Holy See would look benignly on the project. After the death of Pope Benedict XV (22 January 1922), Cardinal Merry del Val was retained by Pope Pius XI in the role of Secretary of the Holy Office, a post he held until 26 February 1930, when he died in Vatican City, aged 64, during an operation for appendicitis. The funeral took place in St Peter's Basilica on 3 March 1930 and the Cardinal was buried in the crypt. On 31 July 1931, a new tomb, gift of the Spanish government, was dedicated by Cardinal Eugenio Pacelli, the future Pope Pius XII.