Methods for producing biocompatible compositions are provided. The biocompatible compositions include an isocyanate-functional polyurethane prepolymer in combination with a foam control agent. The foam control agent decreases the formation of bubbles and/or foam in the biocompatible composition, thereby enhancing the physical properties of the biocompatible composition. The presence of the foam control agent does not compromise the strength of the biocompatible composition. The compositions prepared by the methods of the present disclosure may be used as adhesives or sealants for medical/surgical uses.