After retiring as a player, Quinteros became a manager at San Lorenzo's youth academy. In 2003 he had a brief spell as first team manager. In 2005 he returned to Bolivia to manage Blooming, team which he took to a national title and his first Aerosur Cup that year. Due to his notorious success, he was offered to manage San Martín de San Juan in the Argentine 2nd division, which he agreed upon. In 2007 he returned to Blooming, the institution where he built up his coaching reputation and became an idol. The following year he won the Aerosur Cup for the second time in his managerial career and guided the team back to the championship finals; however, they lost to Aurora on penalty kicks (3–4) after a draw during regulation time in a decisive third match played at Sucre's Estadio Patria. By January 2009 when his contract expired he decided to move on, and took over La Paz club Bolívar, where he won the Aerosur Cup and the Apertura title. Due to some disparities with the president, Quinteros left the club at the end of the year. By January 2010 he was in charge of Oriente Petrolero. During his stint at Oriente his success continued taking the team to an Aerosur Cup and the Clausura 2010 title. On November 5, 2010 Quinteros was named the new manager of the Bolivian national team. On July 3, 2012 he presented his letter of resignation and called a press conference to announce his imminent departure from the national team. On July 9, Quinteros was formally introduced as the new manager for Ecuadorian club Emelec.