His shock departure comes less than a season after he returned to the Riverside to take over the helm following George Norrie's departure at the end of September.
Somerside guided Garstang to a top four finish this season, and they could still finish third depending on the outcome of Dalton United's game at Blackpool Wren Rovers last night (Tuesday).
This followed on from his time at Garstang last season when, as assistant to manager Gary Hargreaves, he was instrumental in the club's promotion and then the historic West Lancashire League Premier Division title.
Both Somerside and Hargreaves resigned in the summer and George Norrie was appointed the new manager, but lasted only eight games into the campaign with officials saying the appointment was "not working out in the interests of the club.''
Somerside was invited back by chairman Adrian Wilding to 'steady the ship' and he helped lift Garstang up the table, with a record of 12 wins, six draws and six defeats.
He announced his decision to leave prior to the final game of the season on Saturday, which Garstang went on to lose 2-0 at home to bottom club Burnley United.
Somerside has cited increasing family and work commitments for the decision and club officials have been quick to praise his achievements in his two spells at Garstang.
A spokesperson said: "Considering the early season upheaval, the departure of a number of good players, and a continuing injury list, one could only describe the season as a major success and a credit to Scott's management skills in getting the very best out of the people round him, most of all, the players.
"Although Scott may be best remembered for the part he played as Gary Hargreaves' number two, when Garstang FC were crowned as League Champions last season, this season's achievements should never be underestimated. The chairman and committee would like to thank Scott for all his efforts and wish him well for the future.''
Adrian Wilding added: "We tried very hard to keep Scott at the club, but we must respect his decision and move on.
"He knows that he will always be made welcome down at the Riverside at any time in the future. However, nothing stays the same, and it is our job to secure a new manager as soon as possible. It is important that we retain the stability and appoint someone who is capable of building on the work that Scott has done.''