Sodium‐deficient nickel–manganese oxides exhibit a layered structure, which is flexible enough to acquire different layer stacking. The effect of layer stacking on the intercalation properties of P3‐NaxNi0.5Mn0.5O2 (x=0.50, 0.67) and P2‐Na2/3Ni1/3Mn2/3O2, for use as cathodes in sodium‐ and lithium‐ion batteries, is examined. For P3‐Na0.67Ni0.5Mn0.5O2, a large trigonal superstructure with 2√3 a×2√3 a×2 c is observed, whereas for P2‐Na2/3Ni1/3Mn2/3O2 there is a superstructure with reduced lattice parameters. In sodium cells, P3 and P2 phases intercalate sodium reversibly at a well‐expressed voltage plateau. Preservation of the P3‐type structure during sodium intercalation determines improving cycling stability of the P3 phase within an extended potential range, in comparison with that for the P2 phase, for which a P2–O2 phase transformation has been found. Between 2.0 and 4.0 V, P3 and P2 phases display an excellent rate capability. In lithium cells, the P3 phase intercalates lithium, accompanied by a P3–O3 structural transformation. The in situ generated O3 phase, containing lithium and sodium simultaneously, determines the specific voltage profile of P3‐NaxNi0.5Mn0.5O2. The P2 phase does not display any reversible lithium intercalation. The P3 phase demonstrates a higher capacity at lower rates in lithium cells, whereas in sodium cells P3‐NaxNi0.5Mn0.5O2 operates better at higher rates. These findings reveal the unique ability of sodium‐deficient nickel–manganese oxides with a P3‐type structure for application as low‐cost electrode materials in both sodium‐ and lithium‐ion batteries.