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A popular Brooklyn-based organic ice cream chain is planning to soon dish out the final scoops at its flagship store in Boerum Hill.

Alexis Miesen and Jennie Dundas, co-founders of Blue Marble Ice Cream, said today that the chain’s first-ever store at 420 Atlantic Avenue is closing at the end of October after three years in business because the building’s landlord “reneged” on a lease-extension agreement.

Landlord Manuel Fernandez is currently listing the modest storefront for rent with a local broker for $3,500 monthly and claiming the property is 900 square feet.

But Miesen and Dundas said the storefront is actually 670 square feet and that Fernandez squeezed them out by jacking up their rent to $3,800 monthly – double the square-foot price of comparable properties in the neighborhood.

They declined to say what they’re currently paying.

“He claimed he had somebody lined up to pay the new price if we couldn’t,” said Miesen. She added that she doesn’t want to close shop, but it doesn’t make good business sense “to pay such a high rent.”

Blue Marble, which produces its handmade, farm-fresh ice cream Upstate, will continue to operate stores on Court Street in Cobble Hill, Underhill Street in Prospect Heights, as well as satellite shops at Governors Island, Brooklyn Bridge Park, Brooklyn Flea and Central Park’s Summer Stage.

Miesen said she wants to wait until next spring before deciding whether to open a new store, “whether it’s in Boerum Hill or, perhaps, Manhattan.” For now, she and Dundas are planning to expand with wholesale ice cream products for sale at local stores.

Fernandez did not respond to a message seeking comment.

At the Atlantic Avenue store, customers are bummed over the news Blue Marble is closing.

“It seems like a trend here on Atlantic Avenue,” said Chris Enright, 44. “The antique shops and other stores that helped rejuvenate the area are now being driven out.”

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