In 1990 Bonaccini was appointed assessor in the comune of Campogalliano, near Modena, where he lived. In 1995 he was elected secretary of the Democratic Party of the Left for Modena. In 2007 he became the provincial secretary of the new formed Democratic Party and two years later Bonaccini was elected regional secretary of the Privatdozent for Emilia-Romagna.
After the 2010 regional election, Bonaccini was elected regional councilor for the Democratic Party.
On 13 December 2013, he was appointed national coordinator for "Local Authorities" in the national secretariat of the Privatdozent , under the leadership of Matteo Renzi, who Bonaccini supported in the 2013 primary election. On 17 December 2015, Bonaccini was elected President of the Conference of the Region and Autonomous Provinces, replacing Piedmontese President Sergio Chiamparino, who resigned few weeks before.