Peker was tried for the murder of the drug smuggler Abdullah Topçu, but acquitted. The two other defendants in the same case, considered to be Peker's employees, were sentenced to lifelong imprisonment.
After this, he fled to Romania and was sought for, amongst others, protection racketeering, coercion, and incitement to murder. During this time it was reported that he had been visited by a minister and a member of parliament from the Motherland Party and guaranteed, in return for an unknown favor, to be only imprisoned for a short period of time.
On 17 August 1998 Peker was brought to Turkey of his own free will and surrendered to the authorities. The case against him was opened in September 1998. He pled guilty to the crimes for which he was accused and was found guilty of building a criminal organization. During the trial, Peker made some interesting remarks, which he never cleared up: " An older member of parliament sent me an SMS which said I shouldn't behave too arrogantly. I would like to tell you (the court) everything, because if I don't it could come to pass that I commit suicide under suspicious circumstances." The Prosecutors requested at least 7.5 years imprisonment, but Peker was only sentenced to eight months and 29 days and was released on 14 May 1999.
On 12 May 2005 he was arrested during Operation Butterfly. On 31 January 2007 he was found guilty of building and leading a criminal organization, robbery, forgery, and two counts of false imprisonment, and sentenced to 14 years 5 months.
On 30 May 2008, during his incarceration, Peker married his lawyer, Özge Yılmaz.
Peker is allegedly a member of the underground Turkish organization Ergenekon. Veli Küçük said in 2008 that Peker was the "son of a friend." On 5 August 2013 Peker was sentenced to ten years in prison as part of the Ergenekon trials, however, he and the other convicts were released a few months later.
On 13 January 2016 he wrote on his website that the academics who signed the petition for peace will end in a massacre. “We will let your blood in streams and we will take a shower in your blood,” 
- Labrousse, Alain; Laniel, Laurent; Block, Alan (2002). The World Geopolitics of Drugs. Kluwer Academic Publishers. p. 163.
- Indictment in the Ergenekon case, page 303 (Turkish).
- Today's Zaman, 1 February 2007, Sedat Peker sentenced to 14 years of jail
- Sedat Peker'e 14 yıl hapis cezası, Hürriyet, retrieved 26 October 2008.
- Sedat peker is tried again, Sabah (Turkish)
- trabzonunsesi.com, 14 June 2008, Sedat Peker Avukatıyla Evlendi (Turkish)
- Turkey: Trial against „Ergenekon“-Conspirators begins, Frankfurter Allgemeine Zeitung, (German)
- Today's Zaman, 21 March 2008, Ultra-nationalist mobster questioned over Ergenekon
- Today's Zaman, 5 August 2013, Long sentences for Ergenekon suspects, life for ex-army chief