On 27 March 2015, two days before the crucial Euro 2016 qualifier for Greece against Hungary, media reports claimed that Holebas had trained normally with his Roma squad after departing from Austria on Tuesday. "On Monday José underwent a radiographic examination of which it was diagnosed that he was suffering from a left rib case injury. The player trained in Austria under an individual program but was not fit to be available to play against Hungary," the Hellenic Football Federation (HFF) said in an announcement. The HFF added that reports out of Italy cited by the Greek media "lead to completely erroneous conclusions in regards to the willingness of the player to contribute to his commitments with the national team any further." This was probably the cause for the non-call-up of the player for the national team, creating tension with new Greek sporting director and former national team teammate Georgios Karagounis. On 4 September 2015, Holebas returned to the national side after being picked by caretaker coach Kostas Tsanas, where he appeared for Greece for the first time in 12 months in Greece's 0–1 home defeat against Finland in a Euro 2016 qualifier in Piraeus. The defeat officially ended Greece's hopes of qualification to the final tournament in France in a poor overall qualifying campaign for Greece.