Daugherty's tenure of 19 seasons at the helm of the Michigan State Spartans football team is the longest of any head coach in the program's history.

[5] In December 1946, when Munn was hired to become the new head coach at Michigan State University for the 1947 season, Daugherty moved to East Lansing with him.

From 1956 to 1964, Daugherty's Michigan State teams were usually strong, three times placing second in the Big Ten, but never captured the conference crown.

Not wishing to leave Michigan State for a rebuilding program, Daugherty turned it down, but recommended his former assistant, Bob Devaney, for the position.

The 1966 team began the season 9–0 and headed into their final game ranked #2 against #1 Notre Dame at Spartan Stadium on November 19.

Daugherty's teams in the late 1960s and early 1970s consistently hovered around the .500 mark, with only his 1971 squad finishing with a winning record (6–5).

Dissatisfaction from segments of the Michigan State alumni factored into Daugherty announcing on November 3 his resignation as head coach upon the conclusion of the 1972 season.

[10] During Daugherty's time in East Lansing, he recruited and coached 32 All-Americans, some of the best players in Michigan State's history, including Herb Adderley, Brad Van Pelt, Bubba Smith, George Webster, and Joe DeLamielleure.

Daugherty's 109 wins were the most in Spartans history until Mark Dantonio surpassed him in a 31–10 victory over Northwestern at Ryan Field on September 21, 2019.

[11] Daugherty was a color commentator alongside Chris Schenkel and Bud Wilkinson on ABC Sports' college football telecasts beginning in 1973.

The Duffy Daugherty Memorial Award is presented annually to a person for lifetime achievement and outstanding contribution to amateur football.