As a 2014 presidential candidate, Prabowo's past came under renewed scrutiny, with many organisations calling for him to step down. A coalition, which consisted of Imparsial, Kontras, the Setara Institute, and the Human Rights Working Group (HRWG), combined under the Civil Society Coalition Against Forgetting, visited the National Commission on Human Rights (Komnas HAM) in Jakarta on 7 May 2014 to urge the commission to re-investigate Prabowo. A 27 June 2014 report indicated that an investigative journalist, Allan Nairn, had been threatened with arrest "for revealing the former general's role in human rights abuses."
In 2014, the regent of East Kutai, Isran Noor, publicly endorsed Prabowo as a presidential candidate. He also considered pressing criminal charges against Churchill, alleging that Churchill forged its license.
On 22 July 2014, the day that the KPU was due to announce its official tally, Prabowo withdrew from the race after having insisted on his victory since the initial quick counts were released, although the majority showed Jokowi ahead. He attributed this withdrawal to Indonesia "fail[ing] in its duty to democracy" because of "massive cheating that is structured and systematic", and stated that he and Hatta "exercise our constitutional right to reject the presidential election and declare it unconstitutional". His speech, aired live, implied he would challenge the results in the Constitutional Court. Later reports indicated confusion over whether Prabowo had resigned from the election or simply rejected the count.
Following the announcement, the value of the Indonesian rupiah dropped by 0.3%, and the JSX Composite fell by 0.9%. Observers denied Prabowo's allegations of cheating, finding that the elections were "generally fair and free"; Maswadi Rauf of the University of Indonesia stated that there was "no sign of significant fraud", and that Prabowo's withdrawal simply reflected "the real attitudes of the elite, who are not yet ready to accept losing". On 21 August 2014, the Indonesian Constitutional Court rejected his claim of fraud, confirming his election loss.