[2] Uribe insisted that Botero should train in Europe and not in Colombia, so Santiago decided to go to that continent to make his professional debut in 1996 with the Spanish team Kelme.

In October 2004 he joined Phonak, together with Miguel Ángel Martín Perdiguero from Saunier Duval–Prodir, and Víctor Hugo Peña and Floyd Landis from U.S.

[1] On May 1, 2005, he won the Tour de Romandie in Switzerland, 33 seconds ahead of rising Italian star and favorite for the Giro d'Italia Damiano Cunego.

Botero carried that form into the 2005 edition of the Critérium du Dauphiné Libéré when he won the individual time trial ahead of Americans Levi Leipheimer and Lance Armstrong[5] as well as winning the mountainous sixth stage which brought him into second overall in the general classification.

He outlined that his ambitions for the year would be to win the Vuelta a Colombia, to be the Colombian national champion and a podium place in the UCI World championships individual time trial event.

[8] In 2006, Team Phonak dropped him on June 2 after he was named in media reports in the massive Operación Puerto[9] doping probe in Spain, this just weeks before the start of the 2006 Tour de France.

On October 2, 2006, Botero was cleared by the disciplinary committee of the Federación Colombiana de Ciclismo (Colombian Cycling Federation).