The Air Force One project, which Trump complained would cost taxpayers more than $4 billion, invariably arose.
Both CEOs met with Trump within weeks after the President-elect attacked both companies on Twitter for costs on key weapons programmes, including the F-35 and the US Air Force's plan to acquire Boeing 747-8s for the Air Force One presidential transport mission.
The Pentagon has already budgeted $3.2 billion for research and development, military construction and acquisition of two of the Air Force One planes through fiscal 2021, said Kevin Brancato, the lead government contracts analyst for Bloomberg Government.
"Some of the statistics that have been, uh, cited, shall we say, don't appear to reflect the nature of the financial agreement between Boeing and the Department of Defense", he said.
The U.S. Marines and Air Force and six countries use the F-35, which is created to fly at super speeds while avoiding enemy radar.
That what President-elect Donald Trump pledges for the new Air Force One.
Boeing's Muilenburg said he gave Trump a "personal commitment" that the cost of a new one will not get out of control.
Over the summer, the Air Force released its requests for proposals for intercontinental ballistic missiles to replace Boeing's aging Minuteman system.
Mr. Trump also met with Lockheed Martin CEO Marillyn Hewson Wednesday.
Donald Trump has held meetings with the heads of two aerospace companies who lost millions in shares when he criticised their projects for being too expensive.
The meeting comes after Mr. Trump's provocative tweet on December 6, where he said the costs for Boeing's construction of the 747 jet for future commanders-in-chief were "out of control".
Muilenburg also told reporters earlier that he assured Trump that the costs would come down.
Lt. Gen. Christopher Bogdan, the chief of the F-35 Joint Program Office, was one of the generals to meet with Trump on Wednesday, according to multiple reports.
Hewson did not speak to reporters, opting instead to issue a statement through the company.
"We're eager to get started on the program", Muilenberg said. "Primarily the F-35, trying to get the costs down. We're trying to get costs down". "I think Boeing is doing a little bit of a number".