Joe Adams was on target in his last game of the season.
He joined Morecambe until the end of the season on loan from Wigan in January.
They ended the campaign with a 3-3 draw at Swindon Town in a match that Adams cancelled out their opponent's opening goal with a deflected strike.
The Shrimps finished their League Two campaign in 15th, but with off the field problems and having been deducted three points.
Players received their wages late in April, with the club saying that the owner had failed to make funding available on time.
The boss Ged Brennan then announced he was leaving for Accrington Stanley's coaching staff.
"I mean every word when I say it truly saddens me to leave, though I don't see a way in which I could continue given the current situation.
"To be up against what we have been with staffing issues, ownership challenges, the embargo, points deduction and late wages, I couldn't be prouder of what we have achieved this season.
"In light of these challenges, what has become even more apparent to me over the past seven months is just how special this club is, with excellent support inside and out. The fans must stick together more than ever to keep pushing forward."
Adams played 21 games for the club, starting in 17 of those and scoring twice.
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