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.
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