The XCell clinic had been treating disorders including cerebral palsy, Parkinson's disease and spinal cord injury, ScienceMag.org reported Tuesday.
The clinic had been operating under a loophole in European regulations that allowed some treatments already in use when new regulations regarding stem cell procedures took effect to continue for 18 months without formal approval.
The grace period ended in January and German health authorities shut down the clinic in late April. The clinic charged more than 3,000 patients as much as $37,000 each for its treatments.
Authorities are considering criminal charges against the clinic resulting from two cases in which treatments went wrong.
An 18-month-old boy died in October after stem cells were injected into his brain. A few months before, a 10-year-old boy almost died following a similar procedure and is now severely disabled, authorities said.
XCell had clinic branches in Dusseldorf and Cologne.