Giannikis worked as a coach for
Karlsruher SC from 2007 and as assistant manager at the club to
Markus Kauczinski from 2012, until leaving the club in 2016 to follow Kauczinski to
FC Ingolstadt 04, where he was once again Kauczinski's assistant manager. On 14 October 2017, Giannikis was appointed as manager of
Rot-Weiss Essen on a contract until the end of the season. He led Essen to pick up 13 points from the six games between his appointment and the winter break. before it was later announced that he was to become
VfR Aalen manager for the following season. Having suffered hostility from Essen supporters for this decision, he left the club on 7 April 2018 and was immediately succeeded by
Karsten Neitzel. Giannikis was sacked from his role at VfL Aalen on 10 February 2019 after three wins in 22
3. Liga games. In 2019, Giannikis was appointed as the coach of
PAS Giannina. In his first season with the club, he managed to win the
2019–20 Super League Greece 2 title and so the club was promoted to
Super League 1, the top division of Greek football. In
2020–21, he led the team to an 9th-place finish. He also managed to get the team into the semi-finals of the
2020–21 Greek Football Cup for the third time in the club's history after beating
Atromitos and
Panathinaikos. In the semifinals, the club lost to
Olympiacos 2–4 on aggregate. He left the club at the end of the 2020–21 season. Giannikis was appointed as
AEK Athens manager on 10 October 2021, and in December 2021 his contract with the club was extended until 2024. However, he was sacked on 1 March 2022. After leaving AEK, Giannikis returned to Germany and took a break from management, instead spending time with his family. On 20 January 2025, he was dismissed by 1860 Munich. He became the new head coach of
1. FC Saarbrücken on 11 February 2026. ==Personal life==