[1][2] After the coup d'état which followed the 1982 elections, he and fellow colonels César Augusto Cáceres Rojas and Héctor Gramajo Morales — two other Guatemalan officers who had studied counter-insurgency tactics at foreign military schools — created the National Plan of Security and Development.

[3][4] In February 1984, Lobos Zamora was named to the newly created position of Assistant Chief of State under Óscar Humberto Mejía Victores.

[5] He flew to Taipei, Taiwan, that year as his country's official representative at the inauguration of Chiang Ching-kuo to his second term as president of the Republic of China (ROC), demonstrating the close ties between the two anti-communist governments.

[6] His opposition led to a delay of nearly five years in the ROC's plans to establish relations with Belize: in 1984, when then-ROC ambassador to Guatemala Gene Loh travelled to Belize to meet with William Quinto and Prime Minister George Price, Lobos Zamora made his displeasure known, and a CIA agent informed Loh that if the ROC went ahead with its plans, Guatemala might break off relations entirely.

The Grupo de Apoyo Mutuo accused him of human rights abuses and attempted to bring him to trial, but his diplomatic appointment made him immune from prosecution.