Father Duran was highly respected among the Franciscans and as early as 1817 he was recommended for higher offices. In 1824 the College of San Fernando elected him Father-President of the California missions. He held that office three times, 1824-1828, 1831-1838 and 1844-1846. From 1837 to 1843 he was also the comisario prefecto of the Franciscans who were in charge of the southern California missions.
Father Duran had a great love of music and he taught the Indians how to play instruments such as flutes, violins, trumpets and drums. He invented a method of writing the music so the Indians could read it. He created a choir and taught them songs, chants, hymns for the church masses and also created a 30-piece Indian orchestra that was famous throughout the area. It is said that his musical hearing was so sensitive that he could not tolerate even a single string being out of tune and that he would stop the service and wait until the offending string was corrected.
It has also been said that Father Duran made good brandy, which was described as "double distilled and twice as strong as the good father's faith."
Father Duran died at Mission Santa Barbara on June 4, 1846 and was buried in the vault beneath the sanctuary.