From 1979 to 1983, Almaguer served as Deputy Mission Director for the United States Agency for International Development (USAID) in Panama. From 1983 to 1986, Almaguer worked for USAID in Washington, D.C. as Director of the Office of South American and Mexican Affairs. From 1986 to 1990, he served as USAID Mission Director in Ecuador. During the 1990-91 academic year, Almaguer participated in the U.S. State Department's Senior Seminar Program overseen by the U.S. Foreign Service Institute. From 1991 to 1993, Almaguer served as USAID's Regional Mission Director for Eastern Europe, based in Washington. From 1993 to 1996, he served as USAID Deputy Assistant Administrator for Human Resources and Director of Personnel in Washington. From 1996 to 1999, he served as USAID Mission Director in Bolivia.