Batuhan signed a professional contract with Beşiktaş in 2006, after rising through the ranks playing for the youth team. At the beginning of his 2007-08 season, he made his League debut against Kasımpaşa, coming on as a second half substitute for Burak Yılmaz.. His appearance in the match saw him become the youngest ever player ever to feature in a Turkcell Super League match, at the tender age of just 16 years and 115 days. Six days later he scored his first professional goal for Beşiktaş in a 1-0 win against Gaziantepspor on 25 August 2007 scoring in the 95th minute. His goal means he is the youngest playing to score in the League.

He made his Champions League debut in Beşiktaş' 2-0 win against FC Zurich, making a substitute appearance in the 92nd minute, replacing Mert Nobre on 29 August 2007.

On 3 November 2007 Batuhan came on as a substitute for Koray in the 83rd minute against Fenerbahçe. He missed a very crucial chance for Kara Kartallar during the additional time (90+3) as he picked up a loose ball and faked the keeper Volkan, subsequently he tried to shoot despite having had two team-mates unmarked by his side and in the end he could not generate enough power on his shot and Edu cleared the ball away. Beşiktas lost the game with a final score of 2–1 to Fenerbahçe as Sarı Kanaryalar overtook Beşiktaş by one point. Although he was criticized by the Turkish press that he should have assisted Higuain in the match, he stated that he had not seen his team-mate at the time.

During the January 2008 transfer window Beşiktaş wanted to loan him out to F.C. Köln in order for him to get more playing time, however the transfer did not take place due to FIFA rules for each football federation regarding age. According to the German Football Association Karadeniz was classed as a minor and thus could not be transferred as he had a professional contract.

In a later interview that same season for a newspaper, he stated that he missed out on an Istanbul derby match against Galatasaray on 2007–08 season when he did not have even 5 TL to pay and watch at a café.