Prosecutors said Barry Cadden, 50, ran the business in an "extraordinarily dangerous" way by disregarding unsanitary conditions to boost production and make more money.
Cadden, president and co-founder of the now-closed New England Compounding Center, was charged with 25 counts of second-degree murder, conspiracy and other offenses under federal racketeering law.
After five days of deliberations, the jury refused to hold Cadden responsible for the deaths and cleared him on the murder counts. He was found guilty of racketeering, conspiracy and fraud and could get a long prison term at sentencing June 21.
The 2012 outbreak of fungal meningitis and other infections in 20 states was traced by the Centers for Disease Control and Prevention to contaminated injections of medical steroids, given mostly to people with back pain. In addition to those who died, 700 people fell ill. Indiana, Michigan and Tennessee were hit hardest.
Joan Peay, 76, of Nashville, Tennessee, suffered two bouts of meningitis after receiving a shot for back pain. She wept upon learning the verdict.
"He killed people and he's getting away with murder. I am furious," she said. She said that she got so sick from meningitis "I didn't care if I died," and that she still suffers from hearing loss, memory problems, a stiff neck and low energy.
Alfred Rye, 77, of Maybee, Michigan, said: "I wish I could give him the same shot he gave me. I think they should pay for their crime."
Rye fell ill after getting an injection in his lower back 4 years ago. He said he continues to suffer from a loss of balance and other ill effects.
"Life has been totally hell," he said.
The racketeering charge and the 52 counts of fraud carry up to 20 years in prison each, but federal sentencing guidelines typically call for far less than the maximum.
Companies charged with selling contaminated drugs often reach settlements with the federal government and agree to pay large fines. The case against the New England Compounding Center stands apart because of the large number of deaths and serious illnesses and because of evidence that Cadden was aware of the unsanitary conditions, said Eric Christofferson, a former federal prosecutor in Boston.
The scandal threw a spotlight on compounding pharmacies, which differ from ordinary drugstores in that they custom-mix medications and supply them directly to hospitals and doctors. In 2013, in reaction to the outbreak, Congress increased federal oversight of such pharmacies.
Federal prosecutor Amanda Strachan told the jury during the two-month trial that the deaths and illnesses happened because Cadden "decided to put profits before patients."
NECC used expired ingredients and falsified logs to make it look as if the so-called clean rooms had been disinfected, prosecutors said. After the outbreak, regulators found multiple potential sources of contamination, including standing water and mold and bacteria in the air and on workers' gloved fingertips.
Cadden's lawyer, Bruce Singal, told the jury Cadden was not responsible for the deaths and pointed the finger at Glenn Chin, a supervisory pharmacist who ran the clean rooms where drugs were made. Chin has pleaded not guilty and is awaiting trial.
After the verdict, Singal said it was a "disgrace" that prosecutors brought murder allegations against Cadden.
"We're very pleased that the jury acquitted Barry on all 25 of the murder charges and that he can now go home and tell his children that he's not a murderer," Singal said. "At the same time, it is Barry's fervent wish ... that people still remember the victims of this terrible public health outbreak."
NECC filed for bankruptcy after getting hit with hundreds of lawsuits. NECC and several related companies reached a $200 million settlement with victims and their families.
Tom Carroll, a lawyer for the family of Kentucky Judge Eddie C. Lovelace, who died after receiving injections to treat neck and back pain, said the family was disappointed by the outcome of the trial.
"They very strongly felt that a murder conviction was in order," Carroll said. "The family thinks he should get the maximum penalty."
Associated Press writers Chris Ehrmann in Lansing, Michigan; Sheila Burke in Nashville, Tennessee; and Bruce Schreiner in Frankfort, Kentucky, contributed to this report.
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