The team said rising costs and difficult trading conditions had made it impossible to continue.
London Shell Co is to close its two barge restaurants in London’s Paddington after nearly nine years of trading.
Its static Grand Duchess boat will run its last service on 28 September while the cruising Prince Regent will set sail for the last time on 13 October.
In a statement, the team said that “substantial increases in maintenance and overhead costs combined with turbulent trading conditions” had made this decision “inevitable”.
“We can’t change the wind, but we can adjust the sails,” they said.
London Shell Co’s fishmonger, restaurant and wine shop on Swain’s Lane on the edge of Hampstead Heath is unaffected and will continue to trade as normal.
London Shell Co was founded in 2016 and received positive reviews from the Observer’s Jay Rayner, who praised its “well priced” and “simple” menus, while Fay Maschler wrote in the Evening Standard that she “loved” her dinner on the boat.
The operator’s team said in a statement: “We will now focus our attention on our Swain’s Lane fishmonger site and landlubber activities. Swain’s Lane continues to go from strength to strength and we’re looking forward to developing this concept and seeing where the next adventure takes us.
“It’s been an honour. The biggest trip of our lives, the greatest thing any of us have achieved in our still fledgling careers. But most importantly, it’s been a boat load of fun.
“We raise a glass to you and to everyone that has ever clambered aboard these vessels.
“We built these businesses from scratch and have been helped along the way by too many to mention. You all know who you are because you’re stitched into the fabric of our lives.”
The group has urged customers who have purchased gift vouchers to get in touch and said they would be honoured at the Swain’s Lane restaurant.