Benjamin Netanyahu has been indicted on charges of bribery, fraud and breach of trust, becoming the first sitting Israeli PM to face criminal charges.
The decision comes hours after Mr Netanyahu abandoned his bid for immunity.
Israel's Attorney General Avichai Mandelblit's office filed the indictment with Jerusalem District Court on Tuesday.
The case has loomed over the prime minister for months and plagued him during both Knesset elections last year. Israelis are to return to the polls on March 2 for the third time in a year, after negotiations failed to produce a workable coalition.
After withdrawing his immunity bid, Mr Netanyahu wrote on his Facebook page he had "decided not to let this dirty game continue".
He said: "In this fateful hour for the people of Israel, when I am in the United States on a historic mission to design the permanent borders of Israel and ensure our security for decades to come, the Knesset is expected to open another exhibition in the circus of removing immunity."
Benny Gantz, leader of the Blue and White party and Mr Netanyahu's rival to be prime minister, said: "Netanyahu will go to trial now, and we must move forward...
"Israelis have a clear choice... No one can run a state and at the same time manage three serious criminal cases for bribery, fraud and breach of trust."
"The story of The State of Israel vs Benjamin Netanyahu is about much more than what appears on the charge-sheet: it’s a showdown between the political elite of right-wing and religious parties, and the legal establishment," journalist Anshel Pfeffer wrote for the JC about the looming case last year.
"And Mr Netanyahu, despite now having failed twice in forming a government, intends to hold on to every shred of power in order to fend off the charges."