Santos began his career in 1967 as a high school coach in Chicago Heights, Illinois. In 1971, he was named the head coach of the women's program at Cal State Hayward. He took over as men's coach at Hayward in 1973. His women's team won the AIAW National Championships in 1972 and his men's program won the NCAA Division II National Championships in 1977.

Under Santos' leadership, the CSS women won the California Collegiate Team championships in 1971 and 1972. In 1973, the AIAW selected him as National Coach of the Year and in 1977, he was named the NCAA Division II National Coach of the Year. Santos was a member of the 1980 Olympic Coaching staff and an assistant coach for the 1983 Pan Am Games.