Rechargeable aqueous Zn-ion batteries (ZIBs) and Zn−air batteries (ZABs) are emerging as possible alternatives to Li-based batteries due to their high safety, low cost, and environmental friendliness. The development of high-performance Zn-based energy storage devices requires highly durable, efficient, and earth-abundant cathode catalysts. We demonstrate the synthesis of a three-dimensional (3D) hybrid heterostructure based on MnO-Co and graphitic carbon and its bifunctional energy storage performance toward an ZIB and ZAB for the first time. The 3D nanoarchitecture of N-doped graphitic carbon (NC)-encapsulated MnO-Co heterostructure (MnO-Co@NC) supported on onion-like graphitic carbon (OLC) is obtained from a manganese- and cobalt-based multimetal complex Mn3[Co(CN)6]2. The NC outer shell is strongly coupled with the inner MnO-Co heterostructure and integrated with OLC. An ZIB device based on the MnO-Co@NC cathode delivers a specific capacity of 192.3 mAh g−1 at a current density of 200 mA g−1 and has excellent cycling stability of 450 cycles with 100% retention of the initial specific capacity at 2000 mA g−1. The mechanism for Zn-ion storage is established. MnO-Co@NC also efficiently catalyzes the oxygen reduction reaction in an alkaline electrolyte and favors the 4e− pathway desired for the fabrication of an ZAB. MnO-Co@NC serves as an efficient air cathode for the ZAB and it delivers a high peak power density and excellent rechargeability for >30 h with high efficiency. The encapsulating graphitic carbon network and OLC support afford excellent charge−discharge cycling stability to the devices.