After leaving Hibernian, Nicholl returned to Cowdenbeath for a second stint as their manager.[16] He led the Blue Brazil to avoid relegation via the Scottish Championship play-offs in the 2013–14 season beating local rivals Dunfermline Athletic in the two-legged final. He led the side to the Fife Cup that season. However a very difficult season followed in 2014–15, which included a joint-record 10–0 defeat to eventual champions Heart of Midlothian.