Making alkali metal vapor cells includes: providing a preform wafer that includes cell cavities in a cavity layer; providing a sealing wafer having a cover layer and transmission apertures; disposing a deposition assembly on the sealing wafer; disposing an alkali metal precursor in the deposition assembly; disposing the sealing wafer on the preform wafer; aligning the transmission apertures with the cell cavities; subjecting the alkali metal precursor to a reaction stimulus; producing alkali metal vapor in the deposition assembly; communicating the alkali metal vapor to the cell cavities; receiving, in the cell cavities, the alkali metal vapor from the transmission apertures; producing an alkali metal condensate in the cell cavity; moving the sealing wafer such that the cover layer encapsulates the alkali metal condensate in the cell cavities; and bonding the sealing wafer to the preform wafer to make individually sealed alkali metal vapor cells in the preform wafer.