Alaboyun joined the Justice and Development Party and was elected as an AKP Member of Parliament for the electoral district of Aksaray in the 2002 general election. During the 22nd Parliament, he served as the Deputy President of the Turkey-EU Joint Parliamentary Committee. He was re-elected as an MP in the 2007 general election and the 2011 general election. He served as the President of the Interparliamentary Belgium friendship group and was also a member of the Turkish delegation to the NATO Parliamentary Assembly from 2002 to 2011. In 2011, he became the Leader of the NATO Parliamentary Assembly Turkish delegation. Due to the three-term limit imposed on AKP parliamentarians, Alaboyun was unable to seek re-election in the June 2015 general election and subsequently stepped down from Parliament.
After the June 2015 general election resulted in a hung parliament, unsuccessful coalition negotiations raised speculation over whether President Recep Tayyip Erdoğan would call an early election in the event that AKP leader Ahmet Davutoğlu was unable to form a government within the given constitutional time of 45 days. As required by the 114th article of the Constitution of Turkey, the calling of a snap general election by the President necessitates the forming of an interim election government, in which all parties represented in Parliament are given a certain number of ministers according to how many MPs they have. If a party refused to send ministers to the interim cabinet, then independents must take their place. Erdoğan called a new general election for November 2015 in late August, with Davutoğlu being tasked with the formation of the interim government. With the main opposition Republican People's Party and the Nationalist Movement Party refusing to send ministers to the cabinet, the 8 ministries that the two parties were entitled to were vacated for independents. As a result, Alaboyun was appointed Minister of Energy and Natural Resources as an independent politician, resigning his AKP membership in order to participate.
Controversy
Although Alaboyun is technically required to be independent of any political party due to his civil service position and his role in the interim election government, he had served as a three-term Justice and Development Party MP from 2002 to 2015, only resigning his party membership so that he could participate in the election government as an independent. His close affiliation to the AKP despite supposedly being an independent resulted in opposition media outlets branding him, as well as numerous other 'independent' cabinet ministers close to the AKP, as 'partisan independents'.