De Greiff was selected by the Supreme Court out of the ternary presented by President César Gaviria Trujillo, which also included Hugo Escobar Sierra and Guillermo Salah Zuleta (his former deputy rector, and subsequent successor at El Rosario University).
The first challenge for de Greiff happened before he even assumed his new position and involved dealing with the conditions of the incarceration of Pablo Escobar, a notorious drug kingpin and boss of the Medellín Cartel who had recently voluntarily surrendered to the authorities, but as the media had shown, was living a life of luxury in his own personal jail La Catedral where he continued running the cartel.
His outspoken remarks against Escobar, someone feared by most politicians and journalists however, popularized him and catapulted him into the media spotlight, as a brave prosecutor who would take a stance against crime and follow the due process of law, a path which would inadvertently render him the most threatened man in Colombia.
[6] Having garnered enough public support, de Greiff went on to readdress controversial cases like those of 6 innocent men jailed in connection with the assassination of Luis Carlos Galán[7] and those involved in the Escobar scandal.
[8] De Greiff was harshly criticized for this program by U.S. and Colombian law enforcement officials who accused him of providing amnesty for criminals.
[10] A kilo of cocaine costs $50 in the trafficking countries and is sold in the consuming countries for $5,000 to $10,000, and so there always will be someone ready to run the risk of the illegitimate business.De Greiff's comments drew swift condemnation from Colombia's President, Cesar Gaviria Trujillo, who rebuked de Greiff in a letter released to the press,[11] and went on to state "Legalization is not the solution, ... our policy against drug trafficking based on prohibition, the strengthening of justice, the exchange of information and international legal cooperation, will remain unaltered.
Speaking before the U.S. Senate Foreign Relations Committee Subcommittee on Terrorism, Jo Ann Harris, Assistant Attorney General for the Criminal Division, called the behavior of de Greiff "most disturbing" and said that it "jeopardized" the U.S. evidence-sharing program with that country.
Senator John Kerry, then chairman of the subcommittee escalated the situation by directly stating that he was "deeply disturbed" by de Greiff's actions.
This led the US Department of State in March of that year to suspend an evidence-sharing program with the Office of the Attorney General citing that his actions suggested a willingness to make accommodations with drug traffickers.
The accusations drew quick condemnation from the Colombian Episcopal Conference, its President Mgr Pedro Rubiano Sáenz defended the bishops and vowed that the Church in Colombia would continue its duty of ministry to all baptised Colombians regardless of their occupation and alluded that what de Greiff was doing was ignoring the basic principle of the Constitution of Colombia which guarantees freedom of religion, and under that principle, bishops, priests or other member of the church can be in communication with its members.
[25] This incident escalated to international proportions when the Vatican's Nuncio to Colombia, Monsignor Paolo Romeo came out in defense of Mgr Gómez Serna and undermined the actions of the Prosecutor by comparing them to the ancient persecutions of the Church, "in other times the Church has seen its people taken to court and even sentenced to death" said the Nuncio and added "The lost sheep cannot return to its herd if one does not look for it.".
After much deliberation, on March 27, 1994, de Greiff announced that his office was not competent to continue the investigations on the bishops and that the cases would be handed off to the Ecclesiastical court.
The Church in Colombia even went on to defend de Greiff from his critics stating that: "At the moment of truth the Prosecutor has wanted to stick to the legislation.
[34] de Greiff consequently retired on August 17[35] and received the Order of Military Merit Antonio Nariño from President Gaviria for his service to the nation.
[41] De Greiff was one of the few Colombian ambassadors who did not resign following the political scandal that directly linked President Samper to drug cartels and guerrilla members.