Army Colonel Jeffery Nance said he would consider the president's remarks as a mitigating factor at sentencing, however, raising the possibility of a lighter punishment.
During last year's presidential campaign, Republican Trump called Bergdahl "a no-good traitor who should have been executed." The defense said the president's more recent remarks about the case showed his opinion of Bergdahl had not changed and unfairly influenced the proceedings.
Nance ruled in court at North Carolina's Fort Bragg, where Bergdahl's sentencing hearing is underway, that no reasonable person would harbor doubt about the integrity of the proceedings due to Trump's comments.
"I am uninfluenced by the president's comments," said Nance, later adding, "However, I will consider the president's comments as mitigating factors."
Bergdahl, 31, faces a maximum penalty of life in prison and a dishonorable discharge after pleading guilty earlier this month to desertion and misbehavior before the enemy.
Prosecutors concluded their case on Monday.
The Idaho native walked off his combat outpost in Afghanistan in June 2009, was captured by the Taliban and spent the next five years in captivity suffering torture, abuse and neglect.
In testimony last week, U.S. service members described the risks and hardships they faced searching for Bergdahl. Several service members were wounded.
Master Sergeant Mark Allen sustained the most serious injuries. He suffered a debilitating brain injury and can no longer speak after being shot in the head during a July 2009 mission to seek intelligence on Bergdahl's whereabouts.
His doctor and wife were the prosecution's final witnesses.
"Instead of being his wife, I'm his caregiver," Shannon Allen said on Monday. "Which doesn't mean I love him any less, but it's a very different dynamic. We can't even hold hands anymore without me prying open his hand and putting mine in."
Bergdahl told Nance at his Oct. 16 plea hearing that he had planned to go to a nearby base to report "critical problems" in his chain of command and never intended to put anyone at risk.
Comment: Curious minds would probably like to hear more about Bergdahl's defense. What "critical problems in his chain of command" was he intending to bring to light?