[2] On 14 March 2007 Obando announced at a press conference held at Unica Catholic University that he had accepted a request made in January by Nicaraguan president Daniel Ortega to preside over the Peace and Reconciliation Commission, which is charged with ensuring the implementation of signed agreements with Nicaraguans who were affected by the civil war of the 1980s.

When asked if the Holy See approved, he said that Pope Benedict in a recent audience had told him to "work for the reconciliation of the Nicaraguan family".

He helped to delegitimize the regime by refusing to accept the Mercedes automobile Somoza gave him and rejecting invitations to attend official state ceremonies.

In a pastoral letter written in June 1979 he spoke in favor of the Sandinistas' use of armed force to overthrow the Somoza regime and encouraged Nicaraguans not to fear socialism.

He opposed the "people's church" (radical clergy who supported liberation theology)[citation needed] and banned the Misa Campesina Nicaragüense (Nicaraguan peasants' mass).

He criticized many of their policies, including military conscription and restrictions of press freedoms, and accused the Sandinistas of human rights violations.

The Sandinistas, who already in July 1984 had expelled ten foreign priests (who had expressed solidarity with another religious figure who had been accused of being a contrarevolutionary), responded by rebuking Obando repeatedly in public forums.

[citation needed] In 2004 Obando suddenly and unexpectedly announced reconciliation with Daniel Ortega in a deal which offered support for the FSLN in return for Ortega's acquiescence to extending the ban on abortion to all cases, as the then government subsequently legislated, and for not pushing for corruption charges against Obando's protege Roberto Rivas (who was subsequently appointed head of the Supreme Electoral Council).