Carl Zeiss Jena were relegated from the 3. Liga in 2012 and finished second in the tier four Regionalliga Nordost in 2013, and third in 2014. In the 2016–17 season they won the Regionalliga Nordost and were promoted to 3. Liga after a play-off win against Viktoria Köln. CZ Jena won the first match in Köln 3–2 and lost the second leg 1–0 at home, but were promoted on the away goals rule. After three seasons in the 3. Liga, the club experienced an underwhelming season and was relegated to the Regionalliga Nordost in June 2020.