A method and kit are provided for the customization of footwear comprising an upper which is partially or totally made of thermoformable material. The method provides for selectively heating the portions made of thermoformable material of the footwear, while leaving the remaining portions of the footwear at a substantially unchanged temperature, and for applying to the thermoformable material portions a pressure sufficient to adapt their shape to the specific morphology of the user's foot. This allows to customize even footwear comprising delicate portions, which would be damaged if subjected to high temperatures. The method may provide for customizing a footbed, partially or totally made of thermoformable material, to the specific morphology of the user's foot sole. The kit is compact, preferably transportable and capable of autonomously carrying out all the steps of the method.