Having started his career at Sturm Graz in 2006 he moved to Germany two years later where he played for Werder Bremen until 2015, and then Premier League club Watford F.C.

Aged 19, Prödl began his professional career playing for Sturm Graz in the Austrian Bundesliga making his debut on 9 December 2006 in a 3–0 loss against SV Mattersburg.

Prödl soon established himself in the first team at Sturm Graz and despite the international commitment[5] and injury,[7] He went on to score three goals in 27 appearances against SV Mattersburg, Red Bull Salzburg[8] and Austria Kärnten.

[11] On 15 July 2008, Prödl moved to Germany to play for Werder Bremen for a transfer fee of €2.5 million, signing a contract until 2012.

[13] Prödl made his Werder Bremen debut in the first round of the DFB-Pokal in a 9–3 win over Eintracht Nordhorn on 9 August 2008.

[15] By the first half of the season, he had appeared in 13 of 17 league matches, also playing in the unfamiliar right-back role in absence of Clemens Fritz.

[18] He scored his first Werder Bremen goal in the second leg of the last 16 of the UEFA Cup in a 2–2 draw against Saint-Étienne, from which the club progressed winning 3–2 on aggregate.

Prödl formed a partnership with Naldo in central defence when they beat Bayer Leverkusen 1–0 in the DFB-Pokal Final.

[21] In the opening game of the 2009–10 season, Prödl played as a centre-back in a 3–2 loss against Eintracht Frankfurt and was sent-off in the last minutes after a second bookable offence.

[23] After three months on the sidelines, he appeared on the substitution bench and made his return to the first team coming on for Naldo in the 76th minute of a 6–0 win over Freiburg on 21 November 2009.

[26] He scored his first European goal on matchday 6 of the Champions League group stage in a 3–0 win over Inter Milan on 7 December 2010.

[39] On 23 February 2013, he was sent-off in the 44th minute of a match against Bayern Munich for a foul on Mario Gómez; Werder Bremen went on to lose 6–1.

In the 2013–14 season, Prödl scored in the club's first match without Thomas Schaaf, which Werder Bremen lost 3–1 to Saarbrücken in the first round of DFB Pokal.

[61] Prödl made his Watford debut in the opening game of the season, making his first start in a 2–2 draw against Everton.

[62] He remained as a first team regular at the start of the season until he was dropped to the bench in late October ahead of a match against Stoke City,[63] and soon suffered a calf injury during international duty with Austria.

[66] Despite being linked with a move to Serie A side Udinese,[67] Prödl remained at the club and regained his first team place under the management of Walter Mazzarri.

[71] On 31 January 2020, the last day of the 2019–20 winter transfer period, Prödl agreed the termination of his contract with Watford which was due to end in summer 2021.