He spent part of his mission as president of the Western Pennsylvania Conference headquartered in Pittsburgh.

[6]: 27  Following his military service, he graduated from Utah State Agricultural College in 1924 in architectural engineering.

He taught advanced mathematics at Utah State Agricultural College during the chairman's sabbatical.

[6]: 36 Franklin Harris asked him to head BYU's engineering department in 1924, but McDonald declined, stating that he was unqualified for the position.

He taught math and physical education part-time at Mission High School while studying at the University of California, Berkeley.

At McDonald's request, he had meetings directly with the board of trustees, not receiving their instructions through a commissioner of church schools.

In 1949, the board of trustees approved a master of theology degree and encouraged graduates to study elsewhere for their doctorate.

[3]: 443  McDonald recruited more professors to teach the more numerous student body, including Hugh Nibley and M. Wells Jakeman.

[3]: 482–484 Ernest Wilkinson suggested that BYU increase the cost of tuition, and McDonald agreed with the idea, but stated that the First Presidency did not wish to burden students with more expensive tuition, despite their anxiety about the LDS Church's increased cost in enrolling so many more students.

The cost to educate each student increased by $55 from 1944 to 1946, and faculty requested and received raises to combat postwar inflation.

In Amanda Knight Hall, doors were locked on the outside and inside after curfew, causing one woman to publicly protest the policy as dangerous in the case of an emergency.

This helped create a more intimate atmosphere for church services, as previous Sunday school classes could exceed 100 students at a time.

[3]: 470–472 McDonald constantly requested additional funding, including emotional appeals, which strained his relationship with the board of trustees.

After prohibiting the student executive council at the Los Angeles State College of Applied Arts and Sciences from discussing the issue, they resigned in protest.

After negotiations, McDonald rescinded the ban on discussing the loyalty oaths and the student executive council returned.

[13] He helped found San Fernando Valley State College in 1956,[14] where he was president of the general faculty 1956–1958.

In 1943, McDonald asked to be released as stake president so he could continue pursuing his doctoral studies.