Transition metal phosphides are a new class of materials generating interest as alternative negative electrodes in lithium‐ion batteries. However, metal phosphide syntheses remain underdeveloped in terms of simultaneous control over phase composition and 3D nanostructure. Herein, M13 bacteriophage is employed as a biological scaffold to develop 3D nickel phosphide nanofoams with control over a range of phase compositions and structural elements. Virus‐templated Ni5P4 nanofoams are then integrated as thin‐film negative electrodes in lithium‐ion microbatteries, demonstrating a discharge capacity of 677 mAh g–1 (677 mAh cm–3) and an 80% capacity retention over more than 100 cycles. This strong electrochemical performance is attributed to the virus‐templated, nanostructured morphology, which remains electronically conductive throughout cycling, thereby sidestepping the need for conductive additives. When accounting for the mass of additional binder materials, virus‐templated Ni5P4 nanofoams demonstrate the highest practical capacity reported thus far for Ni5P4 electrodes. Looking forward, this synthesis method is generalizable and can enable precise control over the 3D nanostructure and phase composition in other metal phosphides, such as cobalt and copper.