[6] However, the outbreak of World War II cut short Cowden's return to Division One, and the club closed down for the duration of hostilities.

While a 1949 League Cup success over Rangers at Ibrox was a highlight of the early post-war period, Cowden struggled to return to the elite level of Scottish football.

A more professional approach was ushered in with the appointment of former Scotland defender Craig Levein, who had begun his playing career with Cowdenbeath, as manager in 1997.

The 2005–06 campaign saw the team achieve their first divisional title win for 67 years with player-manager Mixu Paatelainen when they won the Third Division.

Season 2008–09 saw Danny Lennon's side miss out on promotion in a penalty shoot-out after a scoreless two-legged match and extra time against Stenhousemuir.

Under new manager Colin Cameron,[8] Cowdenbeath immediately regained promotion the following season, winning the league with two games remaining.

[9] The following season they avoided relegation again by defeating local rivals Dunfermline Athletic 4–1 on aggregate in the Championship Play Off final thanks to goals from Kane Hemmings, Greg Stewart and Thomas O'Brien.

Jimmy Nicholl handed in his resignation shortly after the match leaving Colin Nish to rebuild the team for life in Ladbrokes League One.

Nish was unable to stop the slide and Cowdenbeath suffered successive relegations, finishing 9th but being defeated 2–1 on aggregate by Queen's Park in the semi-finals of the play-offs.

[10] They avoided a third consecutive relegation, and dropping out of the SPFL, by winning a play-off against Lowland League champions East Kilbride.

Their opponents were Highland League champions Cove Rangers and Cowdenbeath survived once again thanks to a 3–2 home win following an away goalless draw.