At the start of the 2013–14 season, Compper appeared in the first two matches of the season. However, he was soon on the substitute bench and struggled for a place the first team, as he faced competition in the central defence position. On 23 January 2014, he scored a late winner against Siena in the quarter-finals of the Coppa Italia, as Fiorentina recorded a 2–1 victory. Despite suffering from an injury later in the season, Compper finished his second season, making 19 appearances and scoring once in all competitions.