Kruse began his career with hometown club TSV Reinbek before he joined Hamburg-based SV Vier- und Marschlande in summer 1998. After more than seven years there, he was scouted by Werder Bremen in January 2006. On 4 May 2009, he signed a two-year contract with FC St. Pauli. During the 2011–12 2. Bundesliga, Kruse scored 13 goals and provided six assists as FC St. Pauli finished on 62 points in fourth place, missing out on the promotion playoffs on goal difference.

Following his successful spell with St. Pauli, Kruse was transferred to Bundesliga side SC Freiburg in the summer of 2012. He made his competitive debut for his new club on 18 August 2012 in a DFB-Pokal match against Victoria Hamburg, which ended in a 2–1 victory as Kruse scored the opening goal and provided the assist for Sebastian Freis’s winner. Kruse made his home league debut on 25 August, scoring a goal in Freiburg’s 1–1 draw with 1. FSV Mainz 05. He helped Freiburg claim their first win of the Bundesliga season in their third game on 16 September, netting a goal and providing two assists in an enthralling 5–3 defeat of TSG Hoffenheim.

As of October 2018, he was the player with the longest active penalty scoring streak – 24 goals. He had not missed a single penalty in six years. His streak started on 7 April 2012.

Following a standout season with Freiburg, Kruse signed for Borussia Mönchengladbach on a four-year deal in April 2013. He made his debut for the club in Gladbach’s loss to 3. Liga side Darmstadt 98 in the first round of the DFB-Pokal on 4 August 2013. He managed to score his first goal for the club on 17 August, firing in Gladbach’s first goal in a 3–0 home victory over Hannover 96. Kruse continued his scoring form on 31 August, netting Gladbach’s third goal of a 4–1 home victory over his former club Werder Bremen.

Kruse received his first call up to the senior squad for a friendly against Ecuador on 29 May 2013 in Boca Raton, Florida. He provided the assist for Lukas Podolski’s second goal of the match before being substituted for Dennis Aogo in the 79th minute. The match ended with a 4–2 victory. Kruse scored his first goal for the national team in his second cap, scoring Germany’s second goal in a 4–3 defeat to the United States in Washington, D.C. on 2 June, a game which celebrated 100 years of the United States Soccer Federation. Despite Kruse’s successful league campaign with Gladbach, he was omitted from the 30-man preliminary squad for the World Cup in Brazil.

Kruse is an avid poker player and made it to the final table, finishing third, at the No-Limit 2–7 Draw Lowball event at the 2014 World Series of Poker on 18 June 2014, taking home $36,494 in prize money. In March 2016, Kruse was fined £20,000 and warned of his future conduct by Wolfsburg after it was revealed that he had lost £60,000 worth of poker winnings in the back seat of a taxi.

On 10 May 2015, VfL Wolfsburg signed Kruse on a four-year deal, after activating his release clause of €12 million. He made his debut as a 70th-minute substitute on 1 August in the 2015 DFL-Supercup, and scored in the penalty shootout as Wolfsburg defeated Bayern Munich after a 1–1 draw. On 8 August 2015, Kruse scored his first goal for Wolfsburg in the fourth minute of 4–1 win at Stuttgarter Kickers in the first round of the DFB-Pokal.

During qualification for UEFA Euro 2016, Kruse scored twice in a 7–0 win over Gibraltar on 13 June 2015.

On 2 August 2016, Kruse re-joined Werder Bremen for a second stint at the club. He scored his first goal for the club in his third league appearance on 3 December 2016, in a 2–1 win against Ingolstadt. On 22 April 2017, he scored four goals in one match for the first time in his career as Werder Bremen came back from 0–1 and 1–2 deficits to defeat Ingolstadt 4–2 and maintain a 10-match unbeaten run.

In May 2019, Kruse announced he would not extend his contract and leave the club following the 2018–19 season.

On 28 June 2019, Kruse joined Fenerbahçe on a three-year deal. On 18 June 2020, he terminated his contract with the club citing unpaid wages.

On 6 August 2020, Kruse returned to the Bundesliga joining Union Berlin. On 3 October, he scored his first goal for Union and the game’s opener in a 4–0 win against Mainz 05. He then scored a penalty and assisted two goals in a 3–1 win against 1899 Hoffenheim on 3 November. During a 5-0 win against Arminia Bielefeld on 7 November 2020, he scored a penalty to equalise Hans-Joachim Abel’s Bundesliga record for most penalties scored (16) without a single miss.