After his baseball playing career was over, Nahigian started his collegiate coaching career as a football coach. He was an assistant at Brown from 1949–1972. He also served two stints as an assistant at Harvard, 1973–1975 and 1978–1981.
Baseball
Providence
Nahigian was a successful high school baseball coach in Rhode Island in the 1940s and 1950s, and he was chosen to succeed Robert Murray as Providence's head coach for the start of the 1960 season. Providence then competed as an independent in the NCAA's District 1, which encompassed New England. In his fourth season, 1963, he led Providence to the program's first NCAA Tournament. At the District 1 Regional, the Friars defeated Connecticut in the opening three-game series but fell to Holy Cross in the regional final. In his 19-year tenure at Providence, Nahigian led the Friars to five more NCAA Tournaments and had an overall record of 221-173-2. His best season at Providence was 1973, when the team went 23-6-1 and appeared in its 5th NCAA Tournament. At the District 1 Regional, the team dropped its opening game to Northeastern. It recovered in the losers bracket to beat Massachusetts and Northeastern to reach the regional final. There, it lost to Harvard, 8-1. Nahigian was named the 1973 New England Coach of the Year.
Harvard
Nahigian replaced Loyal Park as Harvard's head baseball coach for the start of the 1979 season. Nahigian was a Cambridge native, attended high school near Boston, and had served as an assistant football coach at Harvard from 1973–1975. He was the unanimous selection of Harvard's search committee, largely due to his success at Providence. Nahigian spent 12 seasons at Harvard, leading the Crimson to three NCAA Tournaments. The Crimson's three NCAA Tournament appearances came at the Northeast Regional in 1980, 1983, and 1984 after it won the EIBLtitle in each of those seasons. The program reached regional finals in 1980 and 1983. In 1985, Harvard shared the EIBL title with Princeton but was defeated in a playoff and did not reach the NCAA Tournament. In 1990, Nahigian's final season, Harvard participated in the first Baseball Beanpot, finishing as the runner-up to Boston College. Nahigian was named the New England Coach of the Year in 1983, 1984, and 1985. In 1989, he received the Jack Butterfield Award.
Head coaching record
Below is a table of Nahigian's yearly records as a collegiate head baseball coach.