On 19 July 2012, Álvarez was chosen to be the executive secretary of the Inter-American Commission on Human Rights (IACHR) for a four-year term, taking the post on 16 August. While serving on the IACHR, the Procuraduría General de la República opened an investigation against him for alleged misuse of funds given by the Mexican government to the IACHR to finance its activities relating to the Ayotzinapa mass disappearance; the investigation was ultimately abandoned.