The Greenhouse Restaurant and Coffee Shop, a café that has stood at 3 Brattle St. for three decades, closed on Monday, becoming the latest independently owned business in Harvard Square to shut its doors.

As chain eateries like the International House of Pancakes (IHOP), Wagamama, and Qdoba open in the Square, independent shops like the Greenhouse that once flourished around Harvard Yard have had difficulty staying in the black.

After owner and founder Joseph A. Nini died several months ago, his wife Kathleen has had a hard time keeping the restaurant in business, according to the couple’s daughter, Tracey N. Gatha, who has helped her mother run the eatery since last December.

In March, the two of them received an eviction notice from the Greenhouse’s property manager, Richard Getz.

“We’re really disappointed,” Gatha said last night. “It’s obviously been there for 30 years, and my dad built it. It was pretty much his heart and soul.”

“We lost him, and now we lost the restaurant. We don’t feel like we were given an opportunity to give a go at it,” she added, noting that some Greenhouse employees were willing to “take a more active role” in managing the shop.

Getz said he did not know that Gatha and Kathleen Nini were trying to keep the business going.

“That’s news to me,” he said when asked about Gatha’s comments. “All I know is that the owner passed away, and they wanted to get out of it. End of the story.”

Jaime L. Kubik, a manager at the Cardullo’s Gourmet Shoppe, located adjacent to the Greenhouse, said he thought it was “very unfortunate that there are a lot of independent shops that can’t manage to stay in business right now because they can’t afford to pay the high rent.”

Kubik added that the management at Cardullo’s, which has been in business since 1950, finds it necessary to “stay on top of the trends of Harvard Square by developing more and more sophisticated taste.”

Denise A. Jillson, the executive director of the Harvard Square Business Association, said that it would be important for Getz to replace the Greenhouse with an independently owned business “in order for Harvard Square to remain unique and interesting.”

Getz also said the space that the Greenhouse had occupied, located across the street from the Harvard Square T stop, will mostly likely be replaced by another independently owned business.

“We’re working with two restaurants right now,” he said. “It might be months before they get opened.”