Seven years after the "Operacion Puerto" doping ring was uncovered, Judge Julia Santamaria on Tuesday sentenced Eufemiano Fuentes to one year in prison for endangering public health.
Fuentes was also banned from practicing sports medicine for four years and was ordered to pay a fine.
The judge also ruled that the blood bags be destroyed, which ruled out any further investigations by the World Anti-Doping Agency or Spain's national anti-doping body.
The court also sentenced former cycling team official Ignacio Labarta to four months in jail. Fuentes' sister Yolanda and former cycling officials Manuel Saiz and Vicente Belda were acquitted.
Defendants who receive sentences of less than two years in Spain generally do not go to prison.
According to the judge, Fuentes' practices were aimed at enhancing athletes performances and, "This is a potential danger to athletes' health," the ruling said.
The defendants were charged with endangering public health instead of doping because it was not a crime at the time of the arrests. A Spanish anti-doping law has since been passed.
The alleged doping network was uncovered on May 23, 2006, when Spanish police raided several apartments and a laboratory in Madrid and seized about 200 bags of blood. Police also arrested doctors, sporting directors and trainers suspected of taking part in the scheme.
Several top cyclists, including the Spaniards Alejandro Valverde and Alberto Contador, Italian Ivan Basso and Germany's Jan Ullrich were implicated.
During the trial, Fuentes said he also had clients in other sports including soccer, tennis and boxing.
Fuentes has 10 days to appeal.
hc/kms (AP, Reuters, dpa)