motivation from Uruguyans Aníbal Ruíz and Luis Cubilla, he started managing Colombian team Once Caldas in 1986. The following year the Colombia Soccer Federation hired him to manage the national team's youth squad and then was quickly promoted to manage the Senior Squad to compete in the 1987 Copa America where they reached third place by beating the host Argentina. During this time, he was also hired to manage his former team Atlético Nacional. Then in 1989 he had his most successful year in his career. He led Atlético Nacional,composed of many Colombian legends, to win the Copa Libertadores for the first time for any Colombian club. Using Atlético Nacional players as a base for the National Team, he qualified the team to the 1990 World Cup after 28 years of absence. In December, he lost the Intercontinental Cup to AC Milan at the last minute of overtime. An upset to what would have been the perfect season. The following year he led Colombia to its best perfermance in World Cup competition by reaching the second round and losing to Cameroon.
After the World Cup, he was hired as coach of Spain's Real Valladolid. In 1993 he was voted as the South American coach of the year by El Pais and he was ranked third in Spanish Newspaper Marca's list of the worlds greatest managers.
He returned to Colombia in 1992. and got his team América de Cali champion of Colombia. In 1993 he got Colombia qualified for a second time in a row to a World Cup, with a historic triumph over Argentina in Buenos Aires by 5-0. That score made Colombia a surprising favorite for the 1994 World Cup, but the performance there was disappointing, as the team was eliminated in the first round, being defeated by such teams as the United States and Romania.
He had later a brief stint as coach of Atlético Madrid and in 1995 he was hired as the trainer of Ecuador National Football Team. After failing to get Ecuador qualified for the 1998 FIFA World Cup, he returned to Colombia to coach Millonarios.
In 1999 he briefly coached Costa Rica, and in 2000 he also coached for a few months Peru. He would later return to coach Colombia for the 2001 Copa América, winning it for the first time. His latest jobs as a coach would include Saudi Arabian side Al-Hilal, where he won the domestic league and the Asian Champions League and a new stint for Colombia and Argentina's Colón de Santa Fe.
Francisco Maturana is considered to be one of the greatest South American coaches of all time and a legend of the Colombian game.
He worked for FIFA as a technical adviser where he has hold various coaching seminars around the world with the likes of Fabio Capello and Cesar Menotti.
In April 2007 Maturana accepted an offer from Argentine Club de Gimnasia y Esgrima La Plata. He directed his first game on April 22, 2007, the derby against Estudiantes de La Plata. In August 2007 Maturana ended his relationship with Club de Gimnasia y Esgrima La Plata