In 1967 Alley became the line coach at Randolph–Macon College in Ashland, Virginia. In his first season, 1967, the Yellow Jackets finished 7–2 and won the Mason–Dixon Conference and Virginia Small College League (VSCL) championships. In his second and final season, 1968, Randolph–Macon achieved the school's only undefeated, untied season, since the football program's inaugural campaign in 1881, and repeated as Mason–Dixon and VSCL champions.
After serving as an assistant for three seasons, Alley was named as the head coach at the University of Louisville for the 1973 season, succeeding Lee Corso. Alley's 1973 Cardinals team was 5–6 in his first year (3–2 in the Missouri Valley Conference (MVC). The team ended the year with a two-game winning streak, posting victories against Furman (35–14) and West Texas State (21–9).
Alley's 1974 Louisville team finished 4–7 (3–2 in the MVC). The team opened the season with three losses, to Memphis State (16–10), Auburn (16–3) and Cincinnati (7–6). The Cardinals won their first two conference games, against Wichita State (14–7) and North Texas State (24–10), before losing to Drake (38–35), Mississippi State (56–7) and the Tulsa (37–7). After a win against Dayton (20–15), Louisville lost to Vanderbilt (44–0) before closing with a victory against West Texas State (10–8). Alley was fired after two seasons and replaced as Louisville's head coach by Vince Gibson.