A system is disclosed for charging a compact vapor cell, including placing an alkali-filled capillary into a reservoir cell formed in a substrate, the reservoir cell in vapor communication with an interrogation cell in the substrate and bonding a transparent window to the substrate on a common face of the reservoir cell and the interrogation cell to form a compact vapor cell. Capillary action in the capillary delays migration of alkali in the alkali-filled capillary from the reservoir cell into the interrogation cell during the bonding.