Prior to his service as commissioner, he played a significant role in the creation of the LDS Church's "released time" seminary system.

His tenure as commissioner also saw creation of the Institutes of Religion and the transfer of nearly all the remaining church schools to control of the states they resided in.

He also faced a crisis in 1930 and 1931 which threatened to end the released time seminary, but the LDS Church education system survived the Great Depression under his leadership.

Joseph was among the first Latter-day Saints from Utah to travel to the eastern United States to seek higher education.

Major scientific discoveries and technological innovations brought the industry out of the era of the lone-prospector and small company mine and mill operation to a world dominated by multi-national corporations working on massive scales, which required a large body of degreed mining engineers, metallurgists, industrial chemists, and other college-educated workers.

[2] In 1913, Merrill successfully attracted funding for a metallurgical research center cooperatively staffed by the university and by the new U. S. Bureau of Mines.

The Utah experiment station funded original research by students, who received fellowships, as well as university faculty and staff members of the U. S. Bureau of Mines.

In 1928, the university determined the funds for mining and metallurgy research were better spent elsewhere, and the cuts caused staff to leave, such as Antoine Marc Gaudin, a leading metallurgical scientist who left for MIT.

Upon hearing his wife relate stories from the Book of Mormon she had learned in a class taught by James E. Talmage, Merrill began to seek means for students attending public high schools to have some form of weekday religious education.

[4]With the successful launch of institute, Merrill's next task was to facilitate the withdrawal of the LDS Church from the field of secular education in the United States.

In a meeting of the Church General Board of Education in February 1929, Merrill was asked to begin the process of closing all of the remaining schools.

When the Idaho legislature rejected an offer to take control of Ricks College, Merrill worked to ensure its survival as a private school, despite seriously diminished funding.

Influenced by this report, the Utah State Board of Education moved to suspend released time privileges statewide.

Merrill worked to ensure the continuation of released time, speaking before the State Board to in an attempt to convince them of the benefits and legality of seminary.

With most of the LDS Church-run schools eliminated by this point, Merrill's action ensured the survival of what would become the dominant form of religious education for the church in Utah.

One of them, future apostle and church president Gordon B. Hinckley, cited Merrill's influence as a major factor in his own financial thinking.