A method for manufacturing a waterproof and vapor-permeable shoe, comprising the steps of: a) providing an upper comprising a lower peripheral flap; b) providing a lining comprising a covering layer of vapor-permeable material, and at least one functional layer of vapor-permeable and waterproof material provided with a lower peripheral flap protruding from the peripheral edge of said covering layer; c) providing an insole comprising a functional support sheet of waterproof and vapor-permeable material; d) providing a three-dimensional last which traces the shape of a foot having dimensions corresponding to the shoe to be manufactured; e) coupling the insole to said last so as to ensure that the upper surface of said insole remains temporarily adhering to the plant of said last; f) fitting said lining on said last and folding back the lower peripheral flap protruding from said functional layer so as to glue it to the bottom surface of the peripheral edge of said functional support sheet by way of an adhesive material; g) fitting said upper on said last above said lining and folding back the lower peripheral flap of the upper so as to glue it by way of said adhesive material to the outer surface of the lower folded back peripheral flap of the functional layer; h) exerting pressure on the insole against the plant of said last to locally compress the peripheral flap of the upper, the peripheral protruding flap of the functional layer and the peripheral edge of said functional sheet against each other, so as to form a waterproof seal; said method being characterized by the fact that: said step a) comprises reducing the thickness of said lower peripheral flap of the upper designed to overlap said peripheral protruding flap of the functional layer, so as to locally thin it; said step g) comprises applying said adhesive material on the contact faces of the upper and of said lining; said step h) comprises the step of carrying out a three-dimensional superficial pressure in order to compress in a single operating the entire outer surface of upper and said insole simultaneously against on all sides of the underlying last. a) providing an upper comprising a lower peripheral flap; b) providing a lining comprising a covering layer of vapor-permeable material, and at least one functional layer of vapor-permeable and waterproof material provided with a lower peripheral flap protruding from the peripheral edge of said covering layer; c) providing an insole comprising a functional support sheet of waterproof and vapor-permeable material; d) providing a three-dimensional last which traces the shape of a foot having dimensions corresponding to the shoe to be manufactured; e) coupling the insole to said last so as to ensure that the upper surface of said insole remains temporarily adhering to the plant of said last; f) fitting said lining on said last and folding back the lower peripheral flap protruding from said functional layer so as to glue it to the bottom surface of the peripheral edge of said functional support sheet by way of an adhesive material; g) fitting said upper on said last above said lining and folding back the lower peripheral flap of the upper so as to glue it by way of said adhesive material to the outer surface of the lower folded back peripheral flap of the functional layer; h) exerting pressure on the insole against the plant of said last to locally compress the peripheral flap of the upper, the peripheral protruding flap of the functional layer and the peripheral edge of said functional sheet against each other, so as to form a waterproof seal; said step a) comprises reducing the thickness of said lower peripheral flap of the upper designed to overlap said peripheral protruding flap of the functional layer, so as to locally thin it; said step g) comprises applying said adhesive material on the contact faces of the upper and of said lining; said step h) comprises the step of carrying out a three-dimensional superficial pressure in order to compress in a single operating the entire outer surface of upper and said insole simultaneously against on all sides of the underlying last.