The chart-topping musician was told the building - proposed for the grounds of his estate in Dennington, north of Ipswich - would be at odds with the character of the local area.
Refusing planning permission, Suffolk Coastal District Council said the design would "be in conflict with the prevailing landscape character, creating the impression of a second village church".
Citing "unsatisfactory visual impacts", the authority went on to say: "This would result in visual conflict with the character of the existing local landscape."
Sheeran had hoped to tie the knot inside the round tower with his fiancée Cheery Seaborn. The pair announced they were engaged in January this year.
The 27-year-old's planning permission application said the building was intended solely for use by its owner - and it would not be hired out.
The document also said: "It is every person's right to be able to have a place of retreat for contemplation and prayer, for religious observance, celebration of key life and family milestones, marriages, christenings and so forth."
The Shape of You singer called in experts to check for great crested newts in his estate after the Suffolk Wildlife Trust said it was possible ponds within the boundaries "could be breeding sites for this species".
Rejecting the plans, the Council also raised concern over the sustainability of the design and the requirement for artificial lighting.
Sheeran is also facing a £75 million pound lawsuit over claims of copying.
A company which holds the rights to Marvin Gaye's Let's Get It On says Sheeran's track Thinking Out Loud is too similar. It is not the first time he has faced legal action of the track. Sheeran has consistently refuted the claims.
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