The 39-year-old will be involved against Southend on Saturday before hanging up his boots after 21 years and more than 500 games for the Shrimps.
“As the season has progressed I have been doing more and more work with the club’s youth team and the workload has become pretty hard to sustain,” he told the club’s official website.
“I want to do all I can to help make the club’s youth team system as good as it can possibly be and I can now give that 100 per cent of my time.
“I’ve loved every minute of my time at Morecambe and I can’t believe how fast the time has gone. I would really like to thank all the fans for the support they have given me over the years and thank the club for all its support to me.”
Morecambe boss Jim Bentley added: “Stewart has been a legend for the club and been an amazing servant.
“He is arguably the best player I ever played with at Morecambe and I’m not sure we will see anyone else make as many appearances for the club again.”