Alves was born on September 15, 1933, in Boa Esperança, Minas Gerais, Brazil. He obtained his Bachelor of Theology (BTh) degree at the Presbyterian Seminary in Campinas, Brazil, in 1957. He went on to obtain a Master of Theology (ThM) from the Union Theological Seminary in New York City, United States, in 1964. After completing this degree, Alves returned to Brazil amidst a US-sponsored military coup against the democratically elected Brazilian government. At the time, the new military regime was attempting to purge Brazil of communist sympathizers. The Presbyterian Church of Brazil provided the new government with the names of six intellectuals to serve as scapegoats and to avert persecution themselves. Immediately upon his return to Brazil, Alves went into hiding. More than forty accusations were made against Alves and others, including claims that they taught that Jesus was sexually involved with a prostitute, celebrated when their children denounced Americans, and were funded by the Soviet Union. Alves reports that these accusations were ineffective, saying, "the positive side of the document was that it was so virulent, that not even the most obtuse could believe that we were guilty of so many crimes." Alves continued to elude government authorities. Within two months of his arrival in Brazil, he returned to the United States covertly with assistance from Brazilian Freemasons and the Presbyterian Church in the United States, which secured an invitation from Princeton Theological Seminary for him to commence doctoral studies there.