As Secretary of State, Bonilla was constitutionally empowered to assume the seat of Governor of Puerto Rico in case that the incumbent was incapable to do so.

Bonilla was appointed Executive Director of the Puerto Rico Ports Authority in early 2005 by Governor Aníbal Acevedo Vilá.

After Marisara Pont Marchese's confirmation was rejected by the House of Representatives of Puerto Rico for the post of Secretary of State, Governor Acevedo turned to Bonilla and nominated him in the summer of 2005 for the position.

However, the Constitution provides that whenever the Governor is unable to carry out his duties, dies, is impeached or resigns, the Secretary of State shall succeed in the post.

[2] On January 2, 2009, after fulfilling the traditional role of serving as the initial Master of Ceremony of incoming Governor Luis Fortuño's Inaugural Ceremonies, he introduced and turned over that role to his successor, former Puerto Rico Senate President Kenneth McClintock, who, coincidentally, was also a fellow Tulane University School of Law graduate.