A package-level, integrated high-vacuum ion-chip enclosure having improved thermal characteristics is disclosed. Enclosures in accordance with the present invention include first and second chambers that are located on opposite sides of a chip carrier, where the chambers are fluidically coupled via a conduit through the chip carrier. The ion trap is located in the first chamber and disposed on the chip carrier. A source for generating an atomic flux is located in the second chamber. The separation of the source and ion trap in different chambers affords thermal isolation between them, while the conduit between the chambers enables the ion trap to receive the atomic flux.