At the start of the 2019–20 season, Emanuelson played in both legs of the UEFA Europa League Second Round match against HŠK Zrinjski Mostar, as FC Utrecht lost 3–1 on aggragate. However, he found his playing time, mostly coming from the substitute bench. In a 3–0 win against PSV Eindhoven on 19 October 2019, Emanuelson set up FC Utrecht's third goal of the game, having came on as a 75th minute substitute. He later contributed three more assists for the club. With his first team opportunities limited, Emanuelson was linked a move to Major League Soccer side Atlanta United to link up with his former Manager, Frank de Boer, but the move was broken down. Following this, he soon received playing time, playing in the centre–back position. However, the 2019–20 Eredivisie and the KNVB Cup, which FC Utrecht reached the KNVB Cup Final, were halted in the Netherlands on 12 March due to the pandemic, which the season was eventually cancelled. At the end of the 2019–20 season, Emanuelson made eighteen appearances in all competitions.