Port City FC have unanimously decided the club will withdraw its affiliation to the Guernsey Football Association.
At a meeting on Thursday they also agreed to apply to join the IAG Business League.
President Nigel Staples told BBC Guernsey: "We have decided to try it out for a year, after which we will reconsider our decision."
Staples said there were concerns over the GFA five-year plan, financial considerations and the 'one club' rule.
"I, on behalf of the club, would like to thank the GFA for our involvement in the leagues since 1991," said Staples.
"I would especially like to thank Neil Laine and Gary Cortez for all their hard work over the past few seasons.
"We wish the GFA well in their plans, but feel it would be to the detriment of our club to participate in the GFA structure, as without the Business and Sunday Leagues involvement the GFA plan cannot work."
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