The Republican nominee, in particular, would enter office having backed a number of positions contrary to the Pentagon and having leveled harsh critiques of military policy and strategy. Though the military is duty-bound to serve its top commander, and officials have refrained from naming the candidate in comments they've made over the past year, analysts predicted a complicated relationship should Trump assume the Oval Office.
"I think there has been a lot of angst about what a Trump administration would look like," Seth Jones, a former adviser to US Special Operations Command, told CNN Wednesday. "His learning curve will be immense."
The former dean of the Army War College, retired Army Col. Jeff McCausland, told CNN's Chris Cuomo Tuesday that "the brain trust of the Republican Party and national security affairs" have all chosen to "repudiate Trump and say he is, in fact, not qualified to be president of the United States."
During an earlier interview with ABC, Trump had said of McCausland: "I'll sit down and I'll teach him a couple of things."
The GOP candidate also has more broadly criticized the US strategy toward ISIS; suggested bringing back torture; called for a drastic rethinking of American military alliances; and floated the possibility of shifting America's nuclear policy to allow for greater proliferation.
"I know more about ISIS than the generals do, believe me," Trump said in November of 2015.
Asked in June he still thinks he knows more about ISIS than Americans generals, Trump told CBS' "Face the Nation," "Well, they don`t know much, because they're not winning."
"What's not clear is whether he actually means what he has said," noted Jones, now with RAND Corp. "If he tries to jam through some of the statements on torture, if he tries to jam through the rethinking of the US relationship with European allies and Pacific allies, I think he is going to face a lot of resistance."
Clinton, too, has taken positions that appear at odds with some of the public positions of the military, particularly regarding the imposition of a no-fly zone in Syria.
"I'm going to continue to push for a no-fly zone and safe havens within Syria not only to help protect the Syrians and prevent the constant outflow of refugees, but to, frankly, gain some leverage on both the Syrian government and the Russians," Clinton said at the third presidential debate.
Not only has President Barack Obama opposed such a move, military leaders have also expressed concerns.
Chairman of the Joint Chiefs of Staff Gen. Joseph Dunford told Congress in September, "For us to control all of the airspace in Syria, it would require us to go to war against Syria and Russia. That's a pretty fundamental decision that certainly I'm not going make."
However, his perspective on some of Trump's proposals has been even harsher.
Asked about the practice of waterboarding suspects and targeting the families of terrorists, Dunford called
such actions illegal, "inconsistent with the values of our nation" and warned they "would have an adverse effect on troop morale."
Trump has said that US allies need to pay more for the deployment of US troops in their territory.
But Gen. Vincent Brooks, commander of US forces in South Korea, told Congress
that it was actually cheaper to station American troops in Korea than back in the US due to financial contributions from the host country -- though Trump was quick to dismiss the general's argument, saying the US should compel allies to pay for the entirety.
More recently, the GOP nominee has butted heads with the military over the Iraqi-led campaign to reclaim the city of Mosul from ISIS.
For weeks, Trump has lambasted
the coalition effort, calling the undertaking a "total disaster" and saying the US and its allies were "bogged-down" there even as defense officials say they are encouraged by the progress being made.
Trump's repeated criticisms have concentrated largely on the amount of information made public about the Mosul fight.
"Did we give Mosul enough advanced notice?" he asked rhetorically during a Monday rally in Grand Rapids, Michigan. "Whatever happened to the element of surprise?"
But the commander of the US-led coalition fighting ISIS, Lt. Gen. Stephen Townsend, pushed back on the assessment, albeit without mentioning Trump directly.
"I don't see any evidence that it's bogged down at all," Townsend told CNN's Michael Holmes. "Whoever is saying that I don't know where they're getting it, I don't see that."
Townsend was also doubtful whether complete secrecy could be maintained during a campaign as big as Mosul.
"It's just really hard to move 40,000 troops into position from you know, from middle Iraq to northern Iraq, and maintain complete secrecy. It's almost next to impossible," he said. "I would tell you I know this: The enemy was surprised."
Despite the differences, though, Trump has maintained that he enjoys widespread support from the military and showed little sign of concern about his relationship with military brass should he become their boss.
"I have been endorsed largely, conceptually at least, by the military," Trump told a local Florida TV station last month.
The military, however, does not endorse candidates.
Trump also hinted that he might replace a significant number of senior military leaders not to his liking.
Asked in September if he would seek a plan for fighting ISIS from generals who he has already claimed to know more than, Trump told NBC, "They'll probably be different generals, to be honest with you."