He also won the Kosovo Superleague three times with FC Ballkani and lead them to qualification for the group stage of UEFA Europa Conference League in 2022–23 and 2023–24.

[1] Daja started his managerial career in 2005 with Elbasani whom he stayed until 2007, helping the club to win the Kategoria Superiore in 2005–06 season.

[5] On 1 November 2016, following the goalless draw against Vllaznia,[6] Daja was released from his contract by club president Refik Halili.

[7] On 3 January 2017, Daja was hired as the new coach of Skënderbeu hours after the departure of Andrea Agostinelli, who was released from the club.

[11] In the second round, Skënderbeu managed a 1–1 draw versus Kairat at Almaty Central Stadium for the first leg; despite being down in the first ten minutes after a Gerard Gohou, the team pushed for an equalizer and got it thanks to a Bakary Nimaga tap-in.

[12] In the second leg, Daja's team won 2–0 to progress to next round 3–1 on aggregate; his decision to play Sebino Plaku for James Adeniyi resulted a success as the striker scored the second goal with a lob.

Daja resigned from his post on 2 September 2024 after the team failed to qualify for a European competition for the third time in a row.