In 1942 he left to accept the position of president at the University of Wyoming.

During his time at the University of Minnesota he oversaw a period of immense growth; enrollment at the school more than doubled in a single year due in large part to returning servicemen using the G.I.

Morrill put forward a plan to expand the campus across the Mississippi River to ensure the university would have room to accommodate the coming generation of baby boomers.

But by the time Morrill became president at Minnesota he was convinced college football had become too professional and actively worked to keep Minnesota and the Big Ten Conference from professionalizing further.

Under his leadership, Minnesota was the only school to vote against the 3 most important Big Ten votes in the immediate post-World War II years: the 1946 and 1950 Rose Bowl Game agreements, and the 1949 legalization of the athletic scholarship.