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Steve Watt has left Margate with the club saying the decision was by mutual consent.
Watt's departure follows a season which saw the Gate finish just one win away from making the Bostik Premier play-offs.
The announcement was made by Margate on Monday with the decision for manager and club to part company apparently prompted by a board meeting on Tuesday May 1.
The club says Mike Sandmann and Steve Brown will manage the team and all 'football related matters' for the foreseeable future.
A statement by Margate said: "The board of directors would like to place on record their thanks to Steve for his hard work and dedication, aiding the development of the football club during his tenure.
"Tasked with helping stabilise the club, Steve’s impact has ensured solid foundations are in place to build upon.
"Everyone at Margate Football Club would like to thank Steve for his immense contribution - he will always remain a respected and highly valued figure at Hartsdown Park."
Watt, 33, succeeded Nikki Bull as boss at Hartsdown in February 2017 having previously been a player and assistant manager at Bostik South side Hastings United.
He was initially appointed Gate boss until the end of that season, a deal which was then extended until May this year.
The former Maidstone United defender quickly set about assembling a squad full of players with experience of National League South and above, many of whom were former team-mates.
Lenny Pidgeley, Frannie Collin, James Rogers, Tom Mills, Jack Evans, Matt Bodkin, Ben Swift and Alex Flisher were among those to come on board although Flisher injured his ACL in Margate's final pre-season game and missed the entire league campaign.
Watt's own expectations were for a top 10 finish in his first full season, and after a slow start, the Blues then strung together several unbeaten runs, one of which saw them win seven successive games in January and February.
That run came during an 11-game unbeaten sequence which looked to have put them on the threshold of the play-offs only for their form to tail off in the final weeks with six successive draws and only one win in the final 12 matches. They also picked up four red cards in successive matches.
Margate ended the season in seventh, but just two points adrift of Leiston, who filled the fifth and final play-off spot.
Only the two promoted clubs, champions Billericay and runners-up Dulwich Hamlet, lost fewer games than Margate's nine but the Blues had 17 draws, more than any team in the division.
They also surrendered a host of points from winning positions by conceding late goals – a factor Watt felt cost his side a tilt at the title.
Watt's role at Hartsdown also included managing the club's post 16 Academy team.
The club revealed ahead of the Watt announcement that keeper Lenny Pidgeley, midfielders Jack Evans and Sam Blackman and striker Jay May had all left on Monday morning with Blackman swiftly being unveiled as a Concord Rangers player the same day.