I am working on a project where the user can cusotmise his/her shoes. I want them to color the individual parts of the shoe which is easy to build (each part of the shoe is its own mesh).
Are you creating the shoe in Blender and saving it as a gltf/glb file? If so, are each of the parts that you want to re-color separate parts? When loading a Blender object, it is possible to parse the various parts and apply different textures to them (I believe each one is treated as a separate mesh). So I expect that there must be a way to parse a Blender object once it has loaded and apply different colors/textures. Maybe you have already solved that problem.
In three.js, you can add decals to a mesh. There is an example in the three.js examples. But I am not 100% sure if you can apply a decal across multiple meshes.
One work-around might be to add a singe mesh to your Blender object that combines all of the parts (perhaps making it slightly larger so there is no interference) and texture it with a transparent texture that you can modify. (You can add textures to Blender objects when you are loading them.) I believe that there are three.js examples that show how you can modify textures within your program.