Matsumoto did not set a sentencing date. That will happen after prosecutors and defense lawyers argue how much, if any, money Shkreli should be ordered to forfeit, and after defense lawyers ask her to overturn the guilty verdicts.
Shkreli, who remains free on $5 million bail, faces a maximum sentence of 20 years in prison.
But he is sure to receive a far-less-severe punishment than that, given his lack of a criminal record, and other factors.
"I think we are delighted in many ways," said Shkreli said outside of the courthouse.
"This was a witch hunt of epic proportions and maybe they found one or two broomsticks but at the end of the day we've been acquitted of the most important charges in this case."
He almost immediately afterward used his new Twitter account, @samthemanTP, to comment on the outcome of the case, and also started a livestream on YouTube from his apartment.
Shkreli's lead lawyer, Benjamin Brafman, told a group of journalists, "I hope tomorrow's reports inform the public that Martin Shkreli went to trial and despite being Martin Shkreli he won more than he lost."
But acting United States Attorney Bridget Rohde, whose office prosecuted Shkreli, said, "We're gratified as we stand here today at the jury's verdict."
"Justice has been served," said Rohde, whose prosecution team next plans to try Shkreli's co-defendant and former business lawyer Evan Greebel this fall.
Brafman said the amount of money Shkreli could be made to surrender would have been much higher if he had been found guilty of ripping off Retrophin, to repay swindled hedge-fund investors.
But Shkreli was acquitted of that charge, conspiracy to commit wire fraud, which Brafman referred to as "the money count."
Brafman said that because the jury found that any loss suffered by Retrophin was either low, or non-existent, as the defense claims, the sentence recommended for Shkreli will be light.
"I think we would love to have a complete sweep but five out of eight counts, not guilty, is in our view a very good verdict especially since count seven, the main count that impacts on the loss in this case, that was the most important count in the case from our perspective," Brafman said.
"And for Martin to be found not guilty of that count is a very, very good result as far as we are concerned," Brafman said.
He noted that Matsumoto will have "enormous discretion" in sentencing Shkreli, who has no criminal history.
Brafman also said, "I think this verdict is a reasonably good verdict under the circumstances ... we are 90 percent pleased."
The charges against Shkreli were unrelated to his decision, while CEO of Turing Pharmaceuticals, to raise the price of the drug Daraprim from $13.50 per pill to $750 per pill in 2015.
The price increase came as he was being investigated for the case that led to his trial.