[5] On the last matchday of the 2018–19 season, having come on as a substitute, Emmanouilidis completed the scoring in a 4–0 defeat of Panetolikos with the rebound from Nikos Giannakopoulos' blocked shot.
[6] With little prospect of first-team football at Panathinaikos after the arrival of Ghayas Zahid and Yohan Mollo, Emmanouilidis joined fellow Super League club Panionios on loan for the 2019–20 season.
[9][10] A week later he scored at the extra time sealing a vital 3–0 home win game against Panetolikos in his club effort to avoid relegation.
[12] On 1 March 2020, Bachana Arabuli spread the ball across the box to Emmanouilidis who calmly tapped it into the empty net with Panagiotis Tsintotas helpless, to open the score in a 1–1 home draw against AEK Athens.
[14][15] The 20-year-old was left out of Ivan Jovanovic's plans at Panathinaikos and sought to find a club, so that he could leave with a regular transfer and not on loan.