In 2023, the United States Department of Homeland Security filed money laundering charges against Bautista for allegedly receiving bribes associated with the 2016 Philippine general election, which were coursed through U.S. accounts.

[citation needed] In August 2010, Bautista was appointed by President Benigno Aquino III as chairman of the Presidential Commission on Good Government.

[5] Bautista is a member of the Consultative Commission on Charter Change, an independent body formed in 2005 by President Gloria Macapagal Arroyo to propose revisions to the 1987 Philippine Constitution.

[9] The camp of losing vice-presidential candidate Bongbong Marcos claimed and presented reports of irregularities in the hash code of the data provided by the COMELEC's transparency server.

[10][11][12] Another accusation claimed by the Marcos camp was the reports of another discrepancy in the data provided by the same transparency server, where the number of votes have been slightly decreased further.

Hours after announcing his intent to resign, the House of Representatives voted 137–75–2 to impeach Bautista from the post amid allegations of unexplained wealth.

[16] Following a tip from the estranged wife of Bautista, the United States government, through the Department of Homeland Security’s Homeland Security Investigations (HSI), filed money laundering and conspiracy charges against Bautista at the United States District Court in the Southern District of Florida on September 19, 2023.

[17] Bautista allegedly received bribes from an unnamed tech company in securing a multimillion-dollar contract related to the 2016 general election.

[18][19] Bautista was also included in the Pandora Papers as incorporator of Baumann Enterprises Limited, a company registered in the British Virgin Islands in 2010.