Silk fibroin is an excellent candidate for biomedical implantable devices because of its biocompatibility, controllable biodegradability, solution processability, flexibility, and transparency. Thus, fibroin has been widely explored in biomedical applications as biodegradable films as well as functional microstructures. Although there exists a large number of patterning methods for fibroin thin films, multilayer micropatterning of fibroin films interleaved with metal layers still remains a challenge. Herein, we report a new wafer-scale multilayer microfabrication process named aluminum hard mask on silk fibroin (AMoS), which is capable of micropatterning multiple layers composed of both fibroin and inorganic materials (e.g., metal and dielectrics) with high-precision microscale alignment. To the best of our knowledge, our AMoS process is the first demonstration of wafer-scale multilayer processing of both silk fibroin and metal micropatterns. In the AMoS process, aluminum deposited on fibroin is first micropatterned using conventional ultraviolet (UV) photolithography, and the patterned aluminum layer is then used as a mask to pattern fibroin underneath. We demonstrate the versatility of our fabrication process by fabricating fibroin microstructures with different dimensions, passive electronic components composed of both fibroin and metal layers, and functional fibroin microstructures for drug delivery. Furthermore, because one of the crucial advantages of fibroin is biocompatibility, we assess the biocompatibility of our fabrication process through the culture of highly susceptible primary neurons. Because the AMoS process utilizes conventional UV photolithography, the principal advantages of our process are multilayer fabrication with high-precision alignment, high resolution, wafer-scale large area processing, no requirement for chemical modification of the protein, and high throughput and thus low cost, all of which have not been feasible with silk fibroin. Therefore, the proposed fabrication method is a promising candidate for batch fabrication of functional fibroin microelectronics (e.g., memristors and organic thin film transistors) for next-generation implantable biomedical applications.