Dr Mark Schmidt, 42, has been sentenced to four years, 10 months for masterminding an international blood doping ring between 2012 and 2019.
Schmidt has also received an additional ban from practising medicine for a further three years and was fined 158,000 euros ($A189,000).
Schmidt has been found guilty of 24 counts of using doping methods and two counts of forbidden use of medicinal drugs.
"You are the head of, what I now call, a 'doping system'," presiding judge Marion Tischler said in Munich.
The sentencing judgment included details on how Schmidt had administered a drug not approved for humans on a female athlete in a "human experiment" which was "beyond any ethical standards".
The trial, which started last September, is the first major prosecution under anti-doping legislation introduced in Germany in 2015.
Blood doping is aimed at boosting the red blood cells, which allows the body to transport more oxygen to muscles, increasing stamina and performance.
Two of Schmidt's four co-defendants were each given suspended sentences of two years, four months and one year, four months.
The other two, one of whom is Schmidt's father, were given fines of 6,560 euros and 9,900 euros.
In court last week, Schmidt expressed remorse, "I took a wrong turn, it's all my fault," and regrets involving his four co-defendants: "I am infinitely sorry that I dragged the other four into it".
Tischler noted Schmidt's cooperation in handing over a Slovenian mobile phone, "a massive help, without which the trial would not have taken place in this form".
Schmidt has been in custody since Austrian and German police swooped during coordinated raids in February 2019, as part of Operation Aderlass - Aderlass translates to 'blood-letting' in German.
There have been allusions within the investigations to further riders under Schmidt's program, with two German cyclists referred to. Some, included acclaimed sprinter Andre Greipel, are calling for the publication of the names of the other riders who doped.
On Tuesday, Austrian cyclist Stefan Denifl became the latest athlete jailed due to the smashing of the Aderlass ring, when he received a two-year sentence, 16 months of which will be suspended.
Kristijan Koren (4 years), Kristijan Durasek (2 years), Alessandro Petacchi (2 years) and Borut Bozic (2 years) were all named in the operation as well, all receiving bans.
Daniel Hondo volunteered his role within the doping ring and hasn't received a sanction as yet, but did lose his job within the Swiss cycling federation.