“It’s a museum that has a very direct connection with Puerto Rico,” Mr. Charpenel said. “But the art world doesn’t come often.”
The new director was friendly and enthusiastic during a recent lunch of Mexican and Latin specialties at El Museo’s Side Park Cafe, occasionally chatting in Spanish with waiters as he described ambitious plans to arrange exhibitions that reflect the varieties of the Latino experience. Ordering a sincronizada — a traditional tortilla-based sandwich — Mr. Charpenel said he would organize panel discussions and publish books to “open a bridge of knowledge” about the cultural contributions of Latinos and to explore subjects like immigration, exclusion and diversity.
“I will try to avoid idealizing our histories and our cultures,” Mr. Charpenel said. “I would instead like to talk about the tensions, contradictions and complexities.”
When Mr. Charpenel was hired in May, El Museo lauded his “global vision.” The country’s oldest museum dedicated to Latin art, El Museo was founded in 1969 by artists and activists to emphasize Puerto Rican cultural contributions but eventually broadened its mission to exhibit the work of Latino, Caribbean and Latin American artists from all backgrounds. Its collection of about 8,000 objects includes pre-Columbian artifacts and 20th- and 21st-century drawings, paintings and sculptures.
But even as it has mounted well received exhibitions, El Museo has faced a rocky road. Arts executives with experience managing cultural institutions have asked whether Mr. Charpenel, who has little fund-raising experience, is prepared for the competitive atmosphere of New York, where behemoth cultural organizations vie for funding and attention.
They have also said that he will have to work to overcome the perception that he is an outsider and newcomer to win the support of the museum’s longtime Puerto Rican constituency.
“I hope that he can reach out and sit on the stoop and talk to people,” said Bill Aguado, who led the Bronx Council on the Arts for nearly 30 years. “I hope that he can walk the streets and get a sense of the passion here.”
Mr. Charpenel was born in Guadalajara in 1967 and earned a master’s degree in philosophy from the university there. He painted into his late 20s, he said, then gravitated toward curating. The first big show that he organized was in 1993 at the Museum of Modern Art in Mexico City, he said, and featured works that commented on climate change.
“I believe that museums are platforms of education, research, experimentation,” he said. “Also sometimes they have to become platforms for political resistance.”
Perhaps his most visible role before coming to El Museo was as the director of Museo Jumex, a showcase for the private collection of Eugenio López Alonso, the billionaire heir to the Grupo Jumex juice fortune.
Mr. Charpenel left in 2015 after the Jumex Foundation, which he also headed, canceled an exhibition by Hermann Nitsch that included a depiction of Christ and his disciples as anatomical figures and canvases splattered with blood and black paint, saying it might upset Mexicans already disturbed by violence in the country.
Mr. Charpenel declined to discuss his experiences at Jumex, saying that he and the institution had picked the right time to part ways.
Alain Servais, a collector in Brussels whom he has known for over a decade, said in an email that Mr. Charpenel had successes at the Jumex but that internal politics there may have been difficult to navigate.
“The Jumex has often resembled the court of a French king where competition is provoked by the Sun King to divide and rule,” Mr. Servais wrote. “In my opinion Patrick is a straightforward, straight-shooting personality and it must have been an awkward novelty to end up in a ‘royal court.’”
El Museo has had its own moments of intrigue since Julián Zugazagoitia, a respected leader, left El Museo in 2010. His successor, Margarita Aguilar, was fired after 18 months. The next director, Jorge Daniel Veneciano, departed after two years.
The upheavals continued this year. In May the museum fired Berta Colón, one of two senior executives who had been temporarily running the institution. She accused the second temporary leader of employee intimidation. Yasmin Ramirez, an ex officio trustee appointed by the de Blasio administration, called for the museum to investigate Ms. Colón’s allegations.
Mr. Charpenel said that he knew of no internal review stemming from the letter by Ms. Colón, who had also told trustees that the museum would face a deficit of $800,000 by the end of their fiscal year. (A spokeswoman for El Museo said the museum ended its 2017 fiscal year with an operating deficit of $44,000.)
In four of the last five years that federal tax filings for El Museo were available, returns show the museum typically took in less than it was spending, with its largest negative net income at $1.9 million, for 2011. Mr. Charpenel said longstanding financial difficulties were on the way to being resolved but did not provide details. He added that he expected that six new board members who had been appointed since his arrival would help to raise money.
One of the new trustees, Veronica Gonzalez-Powell, said she understood that Mr. Charpenel had wanted to add some younger people to El Museo’s board. Ms. Gonzalez-Powell, who is on the board of several Mexican museums, added that she thought that Mr. Charpenel would bring a calming influence to El Museo.
“He’s very down to earth and easy to get along with,” she said. “He can bring people together.”
El Museo, which occupies 6,500 square feet of gallery space inside a 1922 building owned by the City of New York, will undergo extensive renovations. The state and the New York City Department of Cultural Affairs will spend $9.3 million replacing heating and air conditioning systems for its galleries and restoring hand-painted murals in its 564-seat theater. The museum will stage some exhibitions at the SVA Chelsea Gallery and at the Longwood Arts Center in the Bronx. And its cafe facing Fifth Avenue, which will remain open, will display videos by Gordon Matta-Clark, an artist with Chilean roots.
Mr. Charpenel added that he also wanted to figure out ways to better use one resource that sets El Museo apart from others: its art-deco theater, El Teatro, which was built in 1924, and will get a new orchestra pit lift and lighting system.
He took a reporter on a tour from the cafe into El Teatro. Gazing at the stained glass ceiling fixtures and the tall oil-on-canvas murals depicting children’s tales like Hansel and Gretel and Cinderella, Mr. Charpenel, paused, visualizing the changes the renovation would bring.
“This theater is a gem,” he said. “We just have to make it shine.”