The challenges associated with synthesizing expanded semiconductor frameworks with cage-like crystal structures continue to be of interest1, 2. Filled low-density germanium and silicon framework structures have distinct properties that address important issues in thermoelectric phonon glass–electron crystals3, superconductivity4 and the possibility of Kondo insulators5. Interest in empty framework structures of silicon and germanium is motivated by their predicted wide optical bandgaps of the same magnitude as quantum dots and porous silicon, making them and their alloys promising materials for silicon-based optoelectronic devices6, 7. Although almost-empty Na1-xSi136 has already been reported8, 9, the synthesis of guest-free germanium clathrate has so far been unsuccessful. Here we report the high-yield synthesis and characteristics of germanium with the empty clathrate-II structure through the oxidation of Zintl anions in ionic liquids under ambient conditions. The approach demonstrates the potential of ionic liquids as media for the reactions of polar intermetallic phases.