Harry Greene, who runs the 11-bedroom Bute House Hotel in Rothesay, said he may now have to close the business after sheriff officers served him with the document because he had begun replacing the original sash and case windows with UPVC ones.
Local MSP Michael Russell said the action taken by Argyll and Bute Council was an "astonishing escalation" while the community council said the Mr Greene had the support of hundreds of residents.
The owner said that when he bought the C-listed property two years ago, it was in a poor state and it was obvious the original sash and case windows would have to be replaced as the wood was rotten and they were painted shut.
He applied twice to Argyll and Bute Council to put in UVPC replacements but was refused on both occasions. He said the cost of replacing them with sash and case windows, as the council wanted, would be almost three times as much and mean a great deal of maintenance.
He appealed the council's second refusal. But in January a Scottish Government Reporter upheld the council's decision, saying UPVC windows would appear as "a noticeably discordant feature" in the otherwise attr-active and prominent building.
Mr Greene said that owners of other similar properties had gone ahead with work to replace windows and had been given retrospective planning permission. He said councillors considering the case of another guest house, also a listed building, had allowed the new windows.
He decided to start replacing the windows and about half the work was completed before sheriff officers from Greenock served him with the court order on Friday.
He said: "We had to stop work and may yet have to close. But the Isle of Bute Jazz festival starts on May 2 and we are fully booked. We can't let them down."
Mick Common, secretary of the Isle of Bute Community Council said a petition against the council's decision had been signed by more than 1000 Bute residents. He said: "There is a problem in Rothesay with derelict buildings, and he is trying to bring one back to life."
Meanwhile Mr Russell has written to Argyll and Bute's chief executive Sally Loudon saying Mr Greene has the support of the entire island.
He said: "I hope that this astonishing escalation is as a result of over zealous enforcement officers exceeding their remit and that it will be abandoned forthwith while a genuine attempt is made to reach a negotiated solution."
A spokeswoman for Argyll and Bute Council said Rothesay had received funding from Historic Scotland and the Heritage Lottery Fund to help regenerate the town centre, while "preserving and enhancing its unique Victorian buildings". She added: "Ensuring that its historic buildings are maintained is crucial in terms of creating funding opportunities for more regeneration, including both public and private sector investment."
She said that local planning policies helped to achieve this.