The expansion projected that attendance would grow to 400,000 visitors a year, but attendance was flat; it remains about 250,000 people a year. Public and private funding dried up. Other improvements, like a rooftop event space and a 30-space parking lot to accommodate guests, have not been completed. The museum is still seeking a site for the lot, while the rooftop should open by this summer, Ms. Wilchfort said.

Despite financial troubles, museum administrators said the institution remains committed to the underserved, participating in programs so that about 30 percent of visitors enter free annually. New discounted membership packages, now targeted at “caregivers,” can still be taken advantage of by grandparents, museum officials said.

In 2008, the museum’s $7.1 million budget supported a full-time staff of 69 employees. Last year, its budget was down to $5 million, the full-time staff down to 35.

A new president hired in 2009, Georgina Ngozi, who is black, tried to recover from the market crash by bringing boldface names into the museum: Soledad O’Brien headlined one gala. Sweet Honey in the Rock, a Grammy-winning black women’s a cappella group, performed at another honoring the magazine editor Pilar Guzman. Ms. Ngozi, a Brooklyn native who grew up in Bushwick and East New York, enlisted the Rev. Al Sharpton, a childhood friend, to read “Cloudy With a Chance of Meatballs” and “A Net to Catch Time” to children.

In interviews, Ms. Ngozi said she stabilized the museum’s finances through cuts that included 25 layoffs. But her contract was not renewed when it expired in October 2012. Ms. Ngozi said that she was never given a specific reason but that she believed some museum trustees “shortsightedly” lacked confidence in her ability to attract visitors and contributors from far afield of the black churches and organizations that had supported it for decades. “My leaving the museum was not my choice,” she said.

In 2013, seeking more of a turnaround agent, the museum board reached back to Ms. Duitz, who had led the institution in the tumultuous 1990s, when the riots between blacks and Hasidic Jews stigmatized Crown Heights for a generation. While the museum had been the setting then for reconciliation meetings that helped heal the wounds the riots had torn open, on Ms. Duitz’s return, the museum itself increasingly became a subject of conflict.

Former and current workers have shared their concerns with local officials, who have met with museum leaders. Among the allegations were that the museum under Ms. Duitz, who is white, laid off veteran employees with valuable institutional memories — and close ties to groups like the Girl Scouts and the organizers of the West Indian American Day parade — who had long helped to shape programming.