Protein is an ideal alternative to many synthetic components in green and bio-electronic products due to its natural abundance, high flexibility and excellent biocompatibility. Here, we report the development of new renewable thermal management materials based on a stable composite system of biocompatible silk fibroin (SF) protein with a small amount (≤25 vol%) of AlN inclusions. The self-assembly of AlN particles and SF was promoted by water annealing to enhance the hydrogen bonding between the phases to reduce the phonon scattering at the interface. The synthesized protein composites have excellent thermal stability, high mechanical durability and low linear expansion, related in part to the secondary structure of silk protein which can be modulated by changing the AlN content. The physical properties were analyzed and modeled within effective medium theory, and the agreements were reasonable, except for the thermal conductivity which was surprisingly much larger than predicted by the model (e.g. 5 times greater at 15 vol%), which is attributed to the strong interaction between protein and AlN, the high thermal conductivity of AlN, and the continuous network of AlN particles that formed at higher concentrations. This makes proteins excellent candidates for thermally conductive composite materials, which have many emerging applications in implantable biomedical devices, flexible and sustainable sensors, and green heat transfer products.