Almaguer was appointed as Secretary for Administration and Finance at the Organization of American States, the third-ranking position at the OAS, in February 2005, where he served for almost six years. He retired from the OAS position in December 2010. Since retiring from the OAS, Almaguer has served on a number of Boards: He has served since 2012 on the Board of Trustees of the Pan American Agricultural University (aka, Zamorano), serving students from throughout the Americas. He also has served on the Board of the USAID Alumni Association (2012-2016). In 2016, Almaguer was appointed by U.S. Secretary of State John Kerry to serve on the Foreign Service Grievance Board (FSGB), a position to which he was reappointed by Secretary of State Mike Pompeo in 2018. In 2017, Almaguer was elected as a member of the American Academy of Diplomacy.