At first, they heard the sirens. Then, peering out over the country’s main political plaza on Wednesday, Bolivia’s top ministers saw the armored vehicles and troops spilling out their doors. A shiver ran down the interior minister’s spine, she later said.

Within moments, the president, Luis Arce, addressed his inner circle — “We are facing a coup!” — before heading to the presidential palace to confront, face to face, the general trying to remove him from power.

The coup attempt failed, lasting a mere three hours, and ended in the arrest of the general, whose motivation for the attack appeared to be, at least in part, anger over his firing by Mr. Arce the day before.

But it was hardly the end of Mr. Arce’s problem, or the challenges facing Bolivia.

Mr. Arce, 60, a former finance minister, took office in 2020 during a democratic election that seemed to symbolize a new, more hopeful chapter in a country coming off a period of intense political tumult.

Now, beyond a dispute with the former general, Mr. Arce is facing a struggling economy, growing protests, criticism over the jailing of political opponents and division within his own party.

But perhaps his biggest challenge is an ongoing battle with his onetime mentor, former President Evo Morales, a titanic figure in Bolivian politics who had receded from the halls of power — and is now fighting with Mr. Arce over who will be their party’s candidate in the presidential election next year.

Mr. Morales, 64, was the first Indigenous president in a country with a large Indigenous population, a socialist elected in 2006 and a leader in the so-called pink wave of leftist politicians who ran much of South America in the 2000s.

He made history by incorporating broad sectors of Bolivian society into politics, but fled the country amid a disputed election in 2019 and chose Mr. Arce to be the candidate representing his party in a new election held in 2020.

In an interview with The New York Times that year, Mr. Arce characterized Mr. Morales as a “historical figure” in their political movement but said Mr. Morales would have no formal role in his government.

It seemed, at the time, to be a successful transition to power for Mr. Arce, who had served in the Morales administration during years of strong economic growth, fueled by a commodities boom and the country’s vast reserve of natural gas.

But now, after a time in exile, Mr. Morales “is really determined to come back to the presidency,” said Gustavo Flores-Macías, professor of government at Cornell University who focuses on Latin American politics. “He sees that he was ousted in an illegal way and that he has the right to be the candidate again. And Arce sees it very differently.”

In Bolivia, a landlocked nation of 12 million people, Mr. Morales, Mr. Arce and their supporters have long tried to position the country as a leftist counterweight to U.S. power.

The country could also play an outsize role in the battle against climate change because of its vast reserves of lithium, which is crucial to the globe’s shift toward electric cars.

The coup attempt on Wednesday was led by Juan José Zuñiga, who until Tuesday evening was the commander general of the army. In an interview, the interior minister María Nela Prada said that Mr. Arce had fired General Zuñiga after he made political statements in a television interview, where he had insisted that Mr. Morales “cannot be the president of this country again” and implied that the military would enforce this assertion.

Before then, “Zuñiga had been President Luis Arce’s trusted man, his most trusted man with the armed forces,” said Reymi Ferreira, a former minister of defense. The general’s dismissal, however, seemed to change that.

The next day, at about 3 p.m., General Zuñiga appeared in the country’s main political square — the home of both the presidential palace and a key government building called the Casa Grande del Pueblo — with the heads of the navy and air force, as well as scores of soldiers.

Mr. Arce and his ministers were in the Casa Grande preparing to begin a meeting, Ms. Prada said, and watched, stunned, as military personnel took over the plaza below.

Mr. Arce, in a black puffy jacket and spectacles, marched to the presidential palace, where, with Ms. Prada at his side, he confronted the general, who wore his green uniform and a bullet-resistant camouflage vest. A crowd of military police surrounded them.

“This is your captain!” Ms. Prada yelled, referring to the president.

“We cannot turn back!” yelled a Zuñiga supporter.

Mr. Arce told the general to turn around.

“This is an order, general,” he continued. “Are you going to listen?”

“No,” Mr. Zuñiga replied.

Then came a key moment, Ms. Prada said. The head of the air force, apparently having second thoughts, decided to rescind his support for the coup effort, she explained. The police declined to join. And eventually a newly appointed commander general of the army ordered the tanks and troops to retreat.

At least 12 people were injured with firearms during the fray, according to Ms. Prada. Seventeen people, including Mr. Zuñiga, are now under arrest. And about 200 military officers took part in the attempted coup, Bolivia’s ambassador to the Organization of American States said on Thursday.

But while Mr. Arce, known widely in the country by his nickname, Lucho, succeeded in heading off a coup, getting Mr. Morales to back down could prove more difficult.

A former leader of the country’s coca growers, Mr. Morales still retains some support among voters and members of his party, the Movement for Socialism, or MAS. A recent survey had support for Mr. Arce at 19 percent of respondents and for Mr. Morales at 9 percent.

Mr. Arce can legally run for a second term in next year’s election, set for the second half of 2025. Whether Mr. Morales can is unclear.

Running for more than two consecutive terms is prohibited under Bolivian law. Mr. Morales served three terms as president, successfully lobbying the courts to allow him to run a third time because of a legal loophole. But when he tried to run a fourth time, it resulted in a disputed election and the turmoil that ousted him.

Bolivia’s constitutional court ultimately has the power to decide if Mr. Morales can run again.

Economic problems inside the country include fuel shortages, high inflation and a lack of access to U.S. Dollars. They have provoked protests led by, among others, truck drivers, a constituency that plays an important role in the country’s commerce.

In the legislature, a segment of Mr. Arce’s party has allied with the opposition to block his initiatives. And his critics have faulted him for going after opponents, including a prominent politician, Luis Fernando Camacho, who has been in pretrial detention since December 2022 on sedition and terrorism charges.

Carlos Romero, a former interior minister under Mr. Morales, said that the relationship between the former president and Mr. Arce was now “abysmal,” and that sowing doubt about the legality of Mr. Morales’s candidacy “is part of the government’s political strategy that insists on disqualifying him.”

Mr. Romero said that the coup attempt on Wednesday was “so clumsy and so improvised” that it must have been an “arrangement agreed upon with the national government” — repeating a claim made by Mr. Zuñiga just before his arrest that the coup attempt was a stunt concocted by Mr. Arce to make him look like a hero.

Mr. Arce’s government has said there is no evidence to back up this claim, and has denied it.

Carlos Mesa, a former president and a leader of the country’s main opposition party, said he believed Mr. Arce was already trying to benefit politically from the coup attempt “by victimizing himself.”

On Wednesday night, Mr. Arce appeared on a balcony overlooking the main political plaza, where hundreds of supporters had gathered, and announced that they had defeated the country’s “coup-plotters.”

“Thank you, Bolivian people!” he yelled.

Then, the crowd erupted: “Lucho! Lucho! Lucho!”

Jorge Valencia contributed reporting.