His involvement in the reform movement continued when he was a member of the General Elections Commission (KPU), the representative of the government, which organized the first democratic elections in 1999. With the establishment of the Ministry of Regional Autonomy in the reform era, Mallarangeng resigned from the KPU and joined as an expert staff of Ministers Country of Autonomy Region (1999–2000). The ministry was later dissolved despite being only 10 months old. He then worked on developing the idea of good governance as the Chair of Policy Committee on Partnership for Governance Reform (2000–2002). He had founded the Democratic Nationhood Party (Partai Persatuan Demokrasi Kebangsaan) with Ryaas Rasyid in 2002.
Mallarangeng quit being a lecturer in October 2004 when he was appointed Presidential Spokesperson by President Susilo Bambang Yudhoyono.
On 7 December 2012, he officially resigned his post as Minister of Youth and Sports of the Republic of Indonesia after he was listed as a suspect in a graft case related to the construction of the Hambalang sports complex in Sentul, Bogor, West Java by the Corruption Eradication Commission (KPK). On 11 January 2013 President Susilo Bambang Yudhoyono appointed Roy Suryo as the new Youth and Sports minister.[4] On 17 October, he was officially detained in the detention center Corruption Eradication Commission. Mallarangeng was officially detained after nearly a year of investigation.
He was sentenced to four years in prison and ordered to pay Rp 200 million. On 21 April 2017, he was released, though he is still expected to report to Sukamiskin Penitentiary.[5]
