Even as a child in the 1960s, Jan Davis felt a twinge of resentment about her hometown, Huntsville, Ala., being overlooked.

Rocket tests rattled windows and doors across town, and everyone seemed to have a familial connection to the work of building the rockets that powered NASA’s mission to put a man on the moon. Still, it was mission control in Houston and Cape Canaveral in Florida that became worldwide symbols of the space race.

So when Ms. Davis drove with her family to watch the Apollo 11 launch, she made a sign for their car: “Look out moon, here comes Huntsville.”

Ms. Davis would take herself to space — on three shuttle missions as a NASA astronaut — while the city worked to be even more central to the aerospace and military industry. It attracted legions of scientists, defense contractors and federal investment. And in the final days of the Trump administration, Huntsville was selected as the permanent home of the United States Space Command.

But this week the Pentagon announced it had reversed that call, instead keeping the headquarters in Colorado Springs. The decision left many in Huntsville smarting at being cast into the outer orbit of influence and questioning whether their city was passed over for political reasons beyond their control.

“To have our selection taken away is demoralizing,” Mayor Tommy Battle said in a statement.

Pentagon officials said keeping the headquarters in Colorado, where it has been temporarily located on a Space Force base shared with NORAD command, was a matter of maintaining military readiness and avoiding a potentially lengthy and costly move.

But some political observers saw the choice of a Democratic-controlled state both as a rejection of the hard-line conservatism in Alabama and a repudiation of its senior Republican senator, Tommy Tuberville, who has blocked hundreds of military promotions over a Pentagon policy that reimburses military personnel who travel to obtain an abortion or fertility care.

“Maybe we’ll learn from it and go on from here,” said the Rev. Dr. Randy B. Kelley, the chairman of the Alabama Democratic Party. “But I think that was a, really, just a once-in-a-lifetime opportunity for the city, and we missed out on it. And I think a lot of that reflects on the caliber of people that we have elected in Alabama.”

The Biden administration’s decision, said Representative Terri Sewell, the lone Democrat representing Alabama in Washington, “bows to the whims of politics over merit.”

“A decision of this magnitude should not be about red states versus blue states, but rather what is in the best interest of our national security,” she added.

Space Command, established in 2019, reports directly to the secretary of defense and coordinates the military’s activities in orbit — which include maintaining constellations of satellites for communications, navigation and spying. Political jockeying for its headquarters was inevitable, as it could bring thousands of uniformed service members, civilian employees and their families — and potentially millions of dollars — into a local economy.

For Huntsville, which has billed itself as the Rocket City, that meant years of lobbying for Redstone Arsenal, a military juggernaut shrouded in trees about a 15-minute drive from downtown. It has long housed billions of dollars in research and development programs as well as NASA’s Marshall Space Flight Center.

Though Alabama has been plagued by high rates of poverty and maternal mortality, struggling schools and a legacy of racism and disenfranchisement, advocates for the northern part of the state, which includes Huntsville, say the region has worked to insulate itself from those trends.

“We have to deal with a perception of what people think happens in the Southeastern U.S.,” said Chip Cherry, the president and chief executive of the Huntsville-Madison County Chamber of Commerce. “They think of other places as being the hubs of this kind of activity, which is not true.”

The foundation for Huntsville’s modern-day identity was the arrival of Wernher von Braun and a team of German scientists in the aftermath of World War II. After von Braun had been the Nazis’ leading missile scientist, Alabama allowed him to delve into his dreams of fueling travel to space. Backed by the White House, his team built the rockets that powered the Apollo missions.

At the time, some suggested that the prominence of that federal program and Redstone Arsenal helped pave the way for state officials to allow Huntsville to become the first city in Alabama to integrate its schools.

A city of nearly 222,000, Huntsville now has some of the highest numbers of engineers and doctorate degrees per capita, with an array of accolades for quality of life. It has fostered specialized engineering programs at multiple colleges and at least one high school.

But when the Air Force announced, days before Donald J. Trump was set to leave office, that it would move the Space Command headquarters to a state where several Republicans had embraced the lies that fomented the Jan. 6, 2021, riot at the Capitol, Colorado officials balked. Months later, Mr. Trump further inflamed tensions, telling a radio show that he had “single-handedly said ‘Let’s go to Alabama.’”

Huntsville’s supporters pointed to a Defense Department inspector general analysis that found Redstone Arsenal was a reasonable choice and they argued that the base in Colorado Springs had ranked lower than other sites.

Representative Mike D. Rogers of Alabama, the chairman of the House Armed Services Committee, vowed to press forward with an investigation in the selection process.

But even after losing out on Space Command, Huntsville residents said there was much to be proud of and a sense that the city would continue its upward trajectory.

While the city has agricultural roots in watercress and cotton production, it is the space legacy that remains the most visible.

There’s the towering 363-foot replica of Saturn V that previews the real rocket inside the U.S. Space and Rocket Center. Hundreds of students still don blue flight suits and flock to weekly space camps at the center, which also serves as a museum.

There’s also Cosmic Christ, a beloved church mosaic that places a rendering of his figure — affectionately known as Eggbeater Jesus for appearing to hover atop a hand-held whisk — against a backdrop of planetary orbit. And then there are the Rocket City Trash Pandas, a minor-league baseball team which renamed itself in 2018 after announcing plans to relocate.

“This city is full of tons of, tons of, smart people. It’s also a place of opportunity,” said Gregg Pohly, 63, who recently retired in Huntsville after a career in the military and defense contract work, keeping a watchful eye on his grandchildren playing galactic-themed mini-golf.

Many local officials declined to say much about the Space Command decision, but the reminder that their city could not be insulated from the politics of the state still chafed for some.

“We do have that last name of Alabama, and we have to consciously sell ourselves,” said Donna Castellano, the executive director of the Historic Huntsville Foundation, in an interview from her office above an old hardware store.

On the floor beneath her, she and her staff had carefully displayed modern-day rocket merchandise and tourist trinkets next to a growing exhibit honoring prominent Black businessmen and suffragists.

“We entice you with the rockets, but we make you stay because we’re such lovely people,” Ms. Castellano said, adding, “I wouldn’t write Huntsville off.”

John Ismay and Karoun Demirjian contributed reporting.