The reaction was not universal. Some in the agency resented the political spotlight Comey had brought on the bureau with his public statements at the center of the Russia and Clinton investigation firestorms.
But many felt loyalty to Comey and appreciated his independence to both sides of the political aisle, especially with critical comments President Donald Trump made about the intelligence community during the campaign and early in his presidency, as well as the former director's efforts to streamline administrative processes.
In the wake of the firing, acting FBI Director Andrew McCabe sought to reassure agents Wednesday that the bureau would continue to do its work, according to two officials familiar with the call.
McCabe spoke via secure conference call with top officials in the FBI's field office around the country Wednesday afternoon, according to the officials. He spoke briefly and told them to focus on the FBI's mission. McCabe also met with Trump at the White House Wednesday afternoon, where White House officials said the President would discuss FBI morale.
Morale problem claim 'inaccurate'
One agent called a CNN reporter in tears Tuesday night to say that FBI morale had never been better under Comey -- and that now it had plummeted. Some said they feel like they've lost a family member.
Despite White House claims that Comey had lost the support of his FBI staff, recent former officials disputed the idea that he had anything but respect.
Recently retired assistant director of the national security branch, Michael Steinbach, who oversaw the Russia probe said the claim that the FBI had a morale problem under Comey is "inaccurate."
Comey is "a man of integrity" who was "a strong leader in the organization and entirely respected with the rank and file across the FBI," Steinbach said. "Of course in any situation you have a variety of viewpoints and it's fair to say not everyone agreed with him, but his reputation was that of a respected leader in the organization."
The move will have consequences with agents, though, another former official said.
"It's pretty damaging, and it's demoralizing, and this move I think further separates what should be everybody kind of on the same team," said a former FBI official who spoke on condition of anonymity due to sensitivities of the situation. "It separates the administration from the intelligence community and law enforcement."
News of the firing came Tuesday evening, and Comey learned of his firing from television as he met with agents in Los Angeles. As the news flashed on TV screens behind him, he joked about it being a prank, then shook agents' hands as he stepped aside to get the news confirmed.
The public embarrassment only compacted the effect on agents, who almost universally agreed the situation was handled inappropriately.
"Nobody could have imagined that it would have been done this way," the former official said. "Not a good situation."
FBI agents are trained to separate personal feelings and politics from their work, and former officials that spoke with CNN, who are still in touch with active agents, said they had no doubt that would continue to be the case.
But while the impact may not immediately hit the mission of agents, the overall morale of the agency could continue be affected.
"I think it'll have a big morale impact," said another former FBI official. "As a former agent, we were the people in the trenches for Comey, his troops, and I think it's safe to say that the general consensus is he was liked within the bureau. ... The FBI is supposed to be somewhat impenetrable or somewhat immune to the politics, but I think unfortunately this shows that that's not always the case."
On Wednesday, the White House said that Comey had lost the confidence of the FBI rank and file, claiming that contributed to the decision to fire him.
When pressed by a reporter about praise for Comey from rank and file agents at the daily briefing, White House spokeswoman Sarah Huckabee Sanders defended the claim.
"We've heard from countless members of the FBI that say very different things," she said. "In fact the President will be meeting with acting Director (Andrew) McCabe later today to discuss that very thing, the morale of the FBI, as well as make an offer to go directly to the FBI people if necessary and appropriate."
The White House offered no further explanation of why it was sure Comey had lost agents' confidence despite evidence to the contrary.
Who is brought in now to lead the FBI will be a key indicator of how investigations into sensitive areas like the probe into Russian meddling in the US election will proceed, the first official said.
"If it's somebody who is going to not be as independent and will listen to what Trump and Sessions want, maybe they move resources away from the investigation to the Russian activities," the official said. "There's no ability within the FBI for agents to run a rogue investigation, it's just not possible."