On the first day of testimony from professional riders before the judge in Madrid, Jaksche's evidence could have a bearing on whether the court decides that Fuentes, who denies doping, and his four fellow defendants violated public health laws.
Jaksche was the first cyclist to admit blood doping in connection with the Puerto investigation, which made it to court last month almost seven years after Spanish police seized anabolic steroids, transfusion equipment and blood bags.
The rider told German magazine Der Spiegel in June 2007 that he had used banned substances over a 10-year period and confirmed that from 2005 he was a client of Fuentes and that going to see him was like "going for an oil change".
As Spain's current anti-doping legislation was not in force in 2006 when the police raids took place, the accused, including Fuentes's sister Yolanda, are being tried for violating health laws and the prosecutor has asked for jail sentences of two years.
Jaksche told the court on Monday that as well as performing blood transfusions, Fuentes had supplied him with banned drugs including the booster erythropoietin (EPO).
He had also given him an unidentified "white powder" to contaminate urine samples, he added.
"It was never about health," Jaksche said. "I knew it was prohibited in sporting terms, legally I don't know."
The proceedings have attracted international scrutiny because anti-doping authorities are hopeful they will finally lead to evidence of wrongdoing by athletes in sports other than cycling being made available.
Fuentes told court last month he had clients in sports including football, tennis, athletics and boxing.
When he offered to identify them Judge Julia Santamaria said she would not prevent him but would also not oblige him to do so, saying it would infringe the rights of those implicated.
Testifying by video link from his training base in Tenerife, Italian rider Ivan Basso told the court on Monday he had blood extracted on three occasions at the clinic of another doctor implicated in the case but never had any reinjected.
Basso, a double Giro d'Italia champion, said he had decided to undergo the blood procedure because of his desire to win the Tour de France in 2006.
Along with other riders linked to Fuentes and his associates, he was excluded from the Tour that year and later served a two-year ban after admitting "attempted doping".
"I dreamed of being the best cyclist ever since I was a child," Basso said.
"Fuentes told me that you could work with your own blood and that it was a valid procedure and I accepted it."
The trial continues on Tuesday and Alberto Contador, the Spaniard stripped of one of his three Tour de France titles after testing positive for a banned substance, is due to testify in court on February 22.
Disgraced American rider Tyler Hamilton is due to give evidence by video link on February 19.