[5] In 2009, Kaiser moved to 1899 Hoffenheim II, which was largely credited to his brother, who knew Markus Gisdol at SC Geislingen.

[10] Kaiser waited for a long time until on 14 May 2011 when he made his debut at TSG 1899 Hoffenheim, coming on as a second–half substitute for Edson Braafheid, in a 3–1 loss against VfL Wolfsburg.

[14] This lasted until late–October when he was replaced by the returning Fabian Johnson and appeared on the substitute bench, as well as, the club's second team for the rest of the season.

[17] Kaiser left TSG 1899 Hoffenheim for RB Leipzig, a club based on Regionalliga Nordost, on 11 July 2012, signing a contract until 2016.

[24] He later captained RB Leipzig again for the second time this season, which came against SV Elversberg on 2 March 2014 and scored, as well as, assisting another goal, in a 2–0 win.

[38] Under his leadership at RB Leipzig, Kaiser helped the club gain promotion to the Bundesliga after beating Karlsruher SC 2–0 on 8 May 2016.

[43] He also made his UEFA Champions League debut, where he played 16 minutes after coming on as a second–half substitute, in a 2–1 loss against Beşiktaş on 6 December 2017.

[45] On 13 May 2018, Kaiser was awarded a testimonial match by RB Leipzig, in honour of him being their longest-serving player after spending six years with the club.

[46] On 1 July 2018, Kaiser signed with Danish Superliga club Brøndby on a two-year contract, reuniting with former Leipzig coach, Alexander Zorniger.

[48] On 8 August 2019, Kaiser scored two goals as Brøndby lost 4–2 in the first leg of the UEFA Europa League qualification match against Portuguese club Braga.

[54] He made his debut on 28 January in a 1–0 away loss to SSV Jahn Regensburg, coming on as a substitute for Marc Stendera in the 59th minute.

[3][56] Before the 2020–21 season, Kaiser was appointed the new team captain of Hannover 96 by head coach Kenan Koçak, succeeding Marvin Bakalorz in that role, as the latter had left for Denizlispor.

[57] On 14 September 2020, Kaiser scored his first goal for the club in a 3–2 away win over Würzburger Kickers in the DFB-Pokal after an assist by Marvin Ducksch.

[60] After a few months he announced that he would indeed return to the world of football, working in the scouting departement of RB Leipzig, the club where he spent the majority of his career.