Baking With Multiple Materials on a single Object - TehMerow/PBR_Bake_Tools GitHub Wiki
It is possible to bake with multiple materials on a single object. It is only slightly faster from the default way blender does it with this add-on
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On the first material of you object, create PBR Bake node and the textures you need with either "Generate PBR Textures Full" or "Generate PBR Textures ORM"
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Make sure you connect all of the outputs that are connected to your Principled Shader to the PBR Bake Node
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Copy the generated textures from step 1 to the second material, add another PBR Bake node to this material and connect outputs to PBR Bake node input, continue for each material
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Connect the PBR Bake output for Base Color to the Material Output node on Each Material and make sure you have the Base Color Output texture selected.
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Setup the baking scene in the PBR Bake Tools panel
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Go to the Bake Panel in the Render Properties, change the bake mode to "Emit" and then press the Bake Button
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Continue this for every material on the object
This process is fairly similar to the vanilla texture baking process in Blender when dealing with multiple materials. The addon speeds up the process a small amount but not by much
This is why it is recommend to use multiple textures to have multiple 'materials' in one object with vertex masking which is covered in the Masking With Vertex Colors Tutorial
Or Baking from Selected Object to Active Object Which is slightly easier than baking multiple materials on a single object
This process also allows you to bake from a higher poly object to a lower poly object and bake the normals from high poly to low poly