The charges come after a lawsuit from Google, which resulted in Uber agreeing to pay £199 million ($245 million) to settle the case.
The spotlight then turned on Levandowski, with the judge overseeing the case making the unusual recommendation to open a criminal probe into his conduct after seeing enough evidence to conclude a theft may have occurred.
Thirty-three charges have been filed against the former engineer, each carrying a penalty of a decade in prison and a fine of £203,000 ($250,000), if he is convicted.
After handing himself in, Mr Levandowksi was bailed with a £1.63 million ($2 million).
The 39-year-old dual national has been forced to surrender both his US and French passports and banned from airports.
Miles Ehrlich, one of Levandowski’s lawyers, maintained his client's innocence in a statement read outside the court.
"He didn’t steal anything, from anyone," Mr Ehrlich said.
"This case rehashes claims already discredited in a civil case that settled more than a year."
Prosecutors said the probe is ongoing but they would not disclose whether Uber and its founding CEO Travis Kalanick are targets.
Google and Uber co-operated in the investigation, they said.
"Silicon Valley is not the Wild West," added John Bennett, the FBI agent in charge of the investigation.
Although Tuesday’s indictment did not charge Uber, it is a stain for a company that has been trying to recover from a series of scandals since jettisoning Mr Kalanick two years ago.
Uber has been hit with a series of issues in recent years, including complaints about rampant internal sexual harassment and a cover-up of a computer break-in that stole personal information about 57 million passengers and 600,000 drivers.
What is Levandowski accused of stealing and what has his response been?
The indictment accuses Levandowski of stealing years of top-secret information, which prosecutors likened to the crown jewels of the Waymo - a Google self-driving car spin-off.
That included breakthroughs in lidar, a key piece of technology that enables self-driving cars to detect what’s around them.
During the previous Waymo trial, Uber's boss conceded the company needed to develop self-driving cars to survive.
He denied he ever resorted to stealing technology from Google, which he believed was an ally until he began to suspect the company intended to launch its own ride-hailing service consisting entirely of its robotic vehicles.
Mr Kalanick also testified his push to build a fleet of self-driving cars for Uber led him to woo Levandowski, who at the time was considered to be a pioneer in robotic vehicles.
Waymo, which spun off from Google in 2016, alleged Levandowski downloaded 14,000 documents containing its trade secrets before he left for Otto.
He claims he downloaded them as an authorised Google employee and never brought those files to Uber or any other company.