Sgt Bowe Bergdahl will face a general court-martial for desertion and other charges.
The US soldier was held for five years by the Taliban in Afghanistan.
General Robert Abrams overruled a previous recommendation that the case be moved to a lower court with a maximum penalty of 12 months of prison.
Sgt Bowe Bergdahl now could be sentenced to life in prison if found guilty.
He was released in exchange for five Taliban officials held at Guantanamo Bay, Cuba, in 2014.
The 29-year-old gave the first public account of his story last week to the podcast Serial.
The podcast ran excerpts of an interview, in which Bowe Bergdahl claims that he left his base without permission in order to create a crisis and highlight poor leadership within his unit.
Bowe Bergdahl’s release, initially cheered by President Barack Obama and other officials, quickly became controversial when critics said it ran contrary to policy against negotiating with terrorists.
With news that the recommendation had been disregarded, his lawyer Eugene Fidell sent an email to reporters on behalf of the defense team saying he “had hoped the case would not go in this direction”.
In the same email, Eugene Fidell called upon leading Republican presidential candidate Donald Trump to “cease his prejudicial months-long campaign of defamation against our client”. Donald Trump has in the past accused Bowe Bergdahl of treason.
Eugene Fidell also asked members of the House and Senate Armed Services Committees to “avoid any further statements or actions that prejudice our client’s right to a fair trial”.
Five Guantanamo detainees were swapped for the soldier, when Bowe Bergdahl was freed in May 2014. He had spent almost five years in Taliban captivity, after he walked off his post in Afghanistan in 2009.
Republicans on the House Armed Services Committee accused President Barack Obama of misleading them over the prisoner swap.
The charges were filed against Bowe Bergdahl in March, and his case was recommended for the lower court in October.
US soldier Bradley Manning “systematically harvested” a vast trove of secret documents to share with WikiLeaks, military prosecutors have said.
At the start of Pvt. Bradley Manning’s court martial, a prosecutor said Osama Bin Laden had received leaked information.
But defense lawyers said Pvt. Bradley Manning, 25, was young and naive when he shared the files with the anti-secrecy site.
He has not denied his role in the leak, and faces up to life in prison if convicted of aiding the enemy.
Earlier this year, Pvt. Bradley Manning pleaded guilty to 10 of the 22 charges against him related to the leaks, but not to the most serious charge.
The Manning-WikiLeaks case is considered the largest-ever leak of secret US government documents. Prosecutors say the disclosures harmed US national interests, while Pvt. Bradley Manning’s supporters say he is a whistle-blowing hero.
In opening statements on Monday at a military courtroom in Fort Meade, Maryland, prosecutor Capt. Joe Morrow called the case an example of what happened “when arrogance meets access”.
Capt. Joe Morrow argued the case was not about a whistleblower’s leak of targeted information.
“This, your honor, this is a case about a soldier who systematically harvested hundreds of thousands of documents from classified databases and then dumped that information on to the internet into the hands of the enemy,” he said.
According to the prosecutor, Pvt. Bradley Manning used his military training to gain the notoriety he craved and attempted to hide what he had done at every step of the process.
He said he would introduce evidence Osama Bin Laden himself had gained access to some of the WikiLeaks information – and had put it to use.
Prosecutors plan to introduce blog entries, a computer, a hard drive and a memory card as evidence against Pvt. Bradley Manning. The military prosecutors will also call witnesses to describe his training and his deployment to Iraq.
In an opening statement, Pvt. Bradley Manning’s lawyer David Coombs said he was “young, naive and good-intentioned” when he arrived in Iraq.
But in late 2009, after an Iraqi died in an attack, he grew disillusioned after seeing his comrades celebrating because no US soldiers had been hurt.
After that incident, Pvt. Bradley Manning began collecting information he thought would “make the world a better place” if public.
“He believed this information showed how we value human life,” David Coombs said.
At the start of Pvt. Bradley Manning’s court martial, a prosecutor said Osama Bin Laden had received leaked information
“He was troubled by that. He believed that if the American public saw it, they too would be troubled.”
The defense lawyer argued that Pvt. Bradley Manning was “selective” in his choice of the hundreds of millions of documents he had access to.
The prosecution’s opening arguments directly relate to the most serious charge against Pvt. Bradley Manning: aiding the enemy. To obtain a conviction, prosecutors must prove Pvt. Bradley Manning acted with intent to aid the enemy and knowingly gave such adversaries US intelligence information.
The prosecution’s argument – that releasing such information on to the internet counts as aiding the enemy – has serious implications for anyone leaking classified information in the future.
The military will aim to show the information was of “great value” to US enemies, but supporters argue all Pvt. Bradley Manning did was make public what should never have been private.
Pvt. Bradley Manning, who was arrested in May 2010 while serving in Iraq, has not denied leaking the documents.
He told a pre-trial hearing in February he divulged the documents to spark a public debate on the role of the US military and foreign policy.
However, prosecutors argue the leaks damaged national security and endangered American lives.
One of the leaked videos shows graphic footage of an Apache helicopter attack in 2007 that killed a dozen people in Baghdad, including a Reuters photographer.
Other documents leaked included thousands of battlefield reports from Afghanistan and Iraq, as well as secure messages between US embassies and the state department in Washington.
Whatever prison sentence Pvt. Bradley Manning receives will be reduced by 112 days, after a judge ruled he had suffered unduly harsh treatment during his initial detention following his arrest.
The soldier chose to have his court martial heard by a judge instead of a jury. It is expected to run all summer.
Judge Col. Denise Lind ruled in May she would close parts of the trial to the public to protect classified material.
Meanwhile, the UK government said on Sunday it was considering a request from Ecuador to hold talks on the future of WikiLeaks founder Julian Assange.
Julian Assange has lived in the Ecuadorean embassy in London for a year, having been granted political asylum there.
He faces extradition to Sweden over s** allegations, which he denies.
What is WikiLeaks?
Website with a reputation for publishing sensitive material
Run by Julian Assange, an Australian with a background in computer network hacking
Released 77,000 secret US records of US military incidents about the war in Afghanistan and 400,000 similar documents on Iraq
Also posted video showing US helicopter killing 12 people – including two journalists – in Baghdad in 2007
Other controversial postings include screenshots of the e-mail inbox and address book of US vice-presidential candidate Sarah Palin