On 3 February 2020, Rapid Wien's fans named Fountas as the best player of 2019 thanks to his excellent performances with the Austrian club. On 16 February, his twelfth goal of the season came after a mistake by opponent player Thanos Petsos in a 2–0 home win game against WSG Swarovski Tirol. On 1 March, Fountas converted a pass from Christoph Knasmüllner to score the second goal in a 3–1 home win game against SV Mattersburg. He would score again on 7 March, benefiting from a serious mistake by Nemanja Rnić and finishing after winning the ball for his 14th goal of the season, in a 2–2 away draw against Wolfsberger AC. On 7 June, after the COVID-19 pandemic had suspended the league, he scored again in a 4–0 win game over SK Sturm Graz. Three days later, he scored the vital goal in a 1–0 away win against LASK Linz. A week later he scored again, sealing another 1–0 away win against TSV Hartberg. On 24 June, he scored a late goal after Ercan Kara's assist, in a disaster 2–7 home loss to league champions Red Bull Salzburg. On 1 July, he scored in his fifth game in a row sealing a vital 3–1 home win game against LASK. Fountas maintained his prolific form with Rapid Vienna until the end of the 2019–20 Austrian Football Bundesliga campaign, registering an haul of 19 goals to help his club earn a berth in the UEFA Champions League qualifiers. Furthermore, Fountas ended the season as the third highest scorer of the Bundesliga in Austria, trailing only Patson Daka (24 goals, RB Salzburg) and Shon Weissman (30 goals, Wolfsberger).