This follows Alan Rose's move from Sharpies to Wanaka and Shelley Duncan's promotion to director of golf at Balmacewen, while Alan Court took over from Andrew Whiley at Chisholm Links recently.
Metcalfe (48) has been at St Clair for 11 years and will continue to live in Dunedin, having recently bought a house in Portobello.
"I will need to find something else to do, but I will retain my PGA membership and continue to coach players,'' he said.
"The club and board have been very supportive as I have had 11 great years at St Clair and still hope to have some involvement with the club.''
"I want to spend more time with my family and when you are tied to a shop for seven days a week, it is hard to find quality family time.''
Metcalfe also cited the difficult retail golfing climate, which has become much tougher with players buying on the internet.
St Clair's board chairman, Peter Lee, said Metcalfe's resignation came as a surprise and the club would now look at possible restructuring options.
"The board will meet next week to decide on how we progress from the current situation,'' Mr Lee said.
"Balmacewen have made changes to their structure and we are still deciding on which option will drive our club forward.''
Mr Lee would not be drawn on whether the board would appoint another professional to fill the vacancy.
Metcalfe has been a professional for 25 years and came from Yorkshire to St Clair in 2005.
Before migrating, Metcalfe was the head professional at Dinsdale Golf Club in Darlington, a position he held for six years.
"I played a lot of golf when I was a trainee professional and the circuit in the United Kingdom was quite lucrative.''
