[12] In 2004, the Oficina Anticorrupción Anti-Corruption Office denounced him, attributing to him "breach of duties, prevarication and influence peddling" for suspicious handling in a case to favor Alderete.

"[13] On 18 July 1994, a car bomb terrorist attack against the Argentine Israel Mutual Association (AMIA) took place in Buenos Aires, killing 85 people and injuring 300 others.

[20] In 2010, in the context of the AMIA case, he was denounced by prosecutor Alberto Nisman, for threats and illegal espionage along with the macro official Fino Palacios and former minister Carlos Corach.

[21] Nisman also denounced Bonadio for the messages of intimidation he received against him, who also put his daughters Iara and Kala at risk,[22] and for wanting to kill him to dislodge him from the AMIA case.

[27] In 2015, he was removed from the Hotesur case because he “violated the right to defense in trial” of Romina Mercado and Lázaro Báez, and acted with “partiality” by not allowing the experts of the parties to review kidnapped documentation.

[28] In 2015, he was charged with the case of money laundering linked to prosecutor Alberto Nisman, where Sara Garfunkel, mother of Nisman, sister of the prosecutor, Judge Sandra Arroyo Salgado, computer technician Diego Lagomarsino and businessman Claudio Picón were investigated as suspected of having participated in the flight of dollars to a Merrill Lynch account in New York, in which there were movements of at least 650 thousand dollars.