Various methods, systems, and apparatus for implementing aspects of the use of alloy anodes in three-dimensional lithium-ion batteries are disclosed, while accounting for volume change that occurs in these alloy anodes during charging and discharging. A three-dimensional lithium-ion battery according to certain embodiments comprises a battery enclosure, and an anode protruding from a first surface within the enclosure, with the anode having a first state and an expanded state, where the volume occupied by said anode is larger in the expanded state than in the first state. A first cathode is separated from the anode along a first direction, and a second cathode is separated from the anode along a second direction. A separator contacts the first cathode, the second cathode, and a portion of the anode. A gap is provided between the anode and the separator, the gap being larger in the first state than in the expanded state.