Many Ballater homes and businesses were badly affected when the River Dee burst its banks in December as Storm Frank battered Scotland.
The venture - aimed at training young people in the kitchen and attracting visitors - is named the Rothesay Rooms.
Prince Charles is known as the Duke of Rothesay in Scotland.
The "pop-up" initiative, to breathe new life into the derelict former Co-op on Netherley Place, is part of Prince Charles' Ballater Flood Appeal, which has raised Â£160,000 since launching in January.
Guests at Tuesday night's opening included private donors who contributed to the flood appeal, and local business owners and councillors.
Prince Charles said the whole idea for the project stemmed from a comment made by local butcher, Barry Florence, following the floods.
He said that Mr Florence had asked him "why don't you put a Highgrove Shop in Ballater?"
HRH said: "That is what really started this whole idea. It was entirely due to my going into Sheridan's butchers to see how they were getting on.
"There has been a lot of effort in the last six months or so since the disastrous floods that did so much damage to poor old Ballater."
Guy Fenton - who will be head chef for the first six months of the enterprise - said the focus would be on "sustainability" and locally-sourced produce.
The restaurant will open in November to allow for staff recruitment. The attached Highgrove Shop will open at the end of this month.
The cost of the Ballater floods clear-up ran into millions of pounds, much of which was for repairing and refurbishing flood-damaged council houses.
Prince Charles has officially opened his own restaurant and gift shop in an Aberdeenshire village which was badly hit by floods.