A method of manufacturing a multi-layer, composite footwear upper having a three-dimensional geometry includes the steps of forming a substantially planar composite sheet from two or more layers, heating the composite sheet, and compression molding the composite sheet into the three-dimensional geometry of the footwear upper. The composite sheet is formed by laminating a first layer of thermoplastic foam to a second layer of thermoplastic urethane (TPU), preferably in the form of a TPU film. A third layer of mesh fabric can be interposed between the first and second layers. The composite sheet is compressed after heating in a mold cavity to achieve the desired three-dimensional geometry. The composite sheet can be compression molded into separate sections which are assembled after molding to form the footwear upper. Alternatively, the composite sheet can be compression molded into a seamless, unitary footwear upper that requires minimal, if any, assembly for completion. The multi-layer composite upper can be applied to a sole to form performance footwear suitable for use in a wide range of conditions.