His debut came on September 14, 1997 with Uruguay club Defensor Sporting and his team won 3–2 against Club Atlético Peñarol. He then spent time in Australia, Spain, and Chile. In 2003 with Chilean club Unión Española, Biscayzacú was named by IFFHS as the fourth leading goal scorer of the world for the year with 31 goals. He has spent time with nine different clubs, most recently with Nacional of Uruguay, where he has the record of being the second player to score a hat-trick in a game versus the archirrival Peñarol. On 6 January 2010, he signed with Associação Portuguesa de Desportos of Brazil.
After a short period in Brazilian club, he signed with Uruguayan club River Plate, and then moved to Colombia, to play for Deportivo Cali.