Abstract NH 4 + ions as charge carriers show potential for aqueous rechargeable batteries. Studied here for the first time is the NH 4 + ‐storage chemistry using electrodeposited manganese oxide (MnO x ). MnO x experiences morphology and phase transformations during charge/discharge in dilute ammonium acetate (NH 4 Ac) electrolyte. The NH 4 Ac concentration plays an important role in NH 4 + storage for MnO x . The transformed MnO x with a layered structure delivers a high specific capacity (176 mAh g −1 ) at a current density of 0.5 A g −1 , and exhibits good cycling stability over 10 000 cycles in 0.5 M NH 4 Ac, outperforming the state‐of‐the‐art NH 4 + hosting materials. Experimental results suggest a solid‐solution behavior associated with NH 4 + migration in layered MnO x . Spectroscopy studies and theoretical calculations show that the reversible NH 4 + insertion/deinsertion is accompanied by hydrogen‐bond formation/breaking between NH 4 + and the MnO x layers. These findings provide a new prototype (i.e., layered MnO x ) for NH 4 + ‐based energy storage and contributes to the fundamental understanding of the NH 4 + ‐storage mechanism for metal oxides.