Hinteregger began playing football shortly before his seventh birthday in 1999 in the youth team of SGA Sirnitz in Albeck, Carinthia in the Feldkirchen District.

In the 2009–10 season, the native Carinthian was also an integral part of the left defensive side of the academy team, for which he appeared in 14 games until the end of March 2010 and scored four goals.

[11] After being promoted to the Red Bull Salzburg reserve team competing in the Second League in early 2010, Hinteregger made his professional debut on 23 April 2010 in the 2–0 away win over FC Dornbirn playing the full match.

[18] After being appointed team captain by Moniz at the beginning of the 2012 spring season,[19] he was dropped from the squad three weeks later for disciplinary reasons after being involved in a party in Salzburg after a home defeat against SV Mattersburg.

[22] After Moniz had resigned in the summer of 2012, Hinteregger became a starting centre-back in the 2012–13 season under new coach Roger Schmidt, and was also sometimes utilised in the defensive midfield.

[33] New coach Peter Zeidler, who had succeeded Hütter in the summer, suspended Hinteregger from the first-team squad after he criticised his teammates and the club ahead of a game against Austria Wien.

[43] Following a 2–0 defeat against Borussia Mönchengladbach on 26 January 2019, Hinteregger publicly criticised head coach Manuel Baum in an interview with Bayerischer Rundfunk.

[46] Under head coach and compatriot Adi Hütter, under whom he had already played in Salzburg, he immediately established himself as a regular starter and featured in the starting eleven in 14 league games by the end of the season, in which he scored one goal.

[2] He was also in the starting lineup in seven Europa League games and, after beating Shakhtar Donetsk, Inter Milan and Benfica, Eintracht made it semi-finals, where they faced eventual winners Chelsea.

In the second leg, Hinteregger put in a man of the match performance despite missing a penalty in the shootout, and was celebrated by his own fans after the end of the game.

In the Europa League in particular, he attracted attention with strong performances and reached the final with his team after victories in the knockout stages against Sevilla, Barcelona and West Ham United.

[54] On 23 June 2022, Eintracht Frankfurt announced the immediate termination of Hinteregger's contract by mutual consent, after which he retired from professional football.

[55] On 15 July 2022, Hinteregger returned to his original childhood club SGA Sirnitz that plays in the Austrian fifth-tier Unterliga Ost.

[56] In January 2025, Hinteregger moves to Austrian Bundesliga club Austria Klagenfurt, where he signed a contract until 2026, making his professional comeback after two and a half years.

[59] In June 2022, two weeks before his retirement, Hinteregger came under fire in the media after it was discovered that he had organized a football event, the "Hinti Cup" in his hometown of Sirnitz, in collaboration with Heinrich Sickl, a far-right politician and former neo-Nazi.