[4] After three years at the club's reserve, Boenisch made his professional debut for Schalke 04 on 11 February 2006, coming on as a substitute in the 86th minute, in a 7–4 home win against Bayer 04 Leverkusen.

[7] On 1 September 2007, he moved to Werder Bremen on an undisclosed fee, believed to be around €3 million and signed a four-year deal that would last until 2011.

[8] Four months after signing for Werder Bremen, he was joined by Schalke teammate Mesut Özil, who suffered the same fate as Boenisch.

He made his debut for the club, coming on as a substitute for Duško Tošić in the 80th minute, as Werder Bremen won 2–1 against Eintracht Frankfurt.

[12] He returned to the starting line-up throughout March and was criticised by the club's fans for passing the ball to opposition player.

[16] Boenisch then made his UEFA Champions League debut, making his first start, in a 0–0 draw against Cypriot side Anorthosis Famagusta.

[27][28] After appearing four times for Bremen's first team throughout August and early September, Boenisch suffered a knee injury that kept him out for six months.

[31] In April, after long talk of negotiations of a contract extension, Boenisch finally signed a new deal that would keep him until 2012.

Boenisch made his first appearance since being injured coming on as a substitute in the 78th minute in a 1–1 draw against Augsburg on 24 March 2012.

[35] In a 2–2 draw against Borussia Mönchengladbach on 10 April 2012, Boenisch received a straight red card early in the game and missed two matches.

[39] On 6 August 2012, Boenisch was handed a trial at English Premier League side Stoke City and started a pre-season friendly for the club against Torquay United and Yeovil Town.

[45] Boenisch made his Bayer Leverkusen debut, playing 45 minutes, in a 3–1 loss against Wolfsburg on 11 November 2012.

[46] Following good appearances, including his first goal against Eintracht Frankfurt on 19 January 2013,[47] he signed a new contract with the Werkself on 4 February 2013 until June 2016.

[61] In a match against Hertha BSC on 5 December 2015, Boenisch received a straight red card, just 18 minutes to the start of the game for a professional foul committed.

[63] After suffering an injury on his muscle,[64] Boenisch made his return to the first team in a 3–3 draw against Augsburg on 5 March 2016.

On 14 November 2006, Boenisch was called up by German under-20 team for the first time and earned his first cap for the side in a 4–1 victory against Austria.

In November 2009, there were rumors that Poland's new national football team coach Franciszek Smuda was interested in the player but Boenisch said that he had made no decision.

[79] Due to lack chances for a future call up to the German senior squad, on 20 August 2010 Boenisch finally decided to play for Poland and received his first call up for matches against Ukraine and Australia[80][81] He made his debut for Poland against Ukraine on 4 September 2010.

[82] In May 2012, Boenisch was called up by Poland national team for the UEFA Euro 2012 squad.