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Nanostructured manganese oxides (MnOx) have shown incredible promise in constructing next-generation energy storage and catalytic systems. However, it has proven challenging to integrate with other low-dimensional materials due to harsh deposition conditions and poor structural stability. Here, we report the deposition of layered manganese dioxide (δ-MnO2) on bilayer epitaxial graphene (QEG) using a simple three-step electrochemical process involving no harsh chemicals. Using this process we can synthesize a 50 nm thick H–MnO2 film in 1.25s. This synthetic birnessite is inherently water-stabilized, the first reported in the literature. We also confirm that this process does not cause structural damage to the QEG, as evidenced by the lack of D peak formation. This QEG heterostructure enhanced MnO2's redox active gas sensing, enabling room temperature detection of NH3 and NO2. We also report on transforming this δ-MnO2 to other MnOx compounds, Mn2O3 and Mn3O4, via mild annealing. This is confirmed by Raman spectroscopy of the films, which also confirms limited damage to the QEG substrate. To our knowledge, this is the first synthesis of Mn2O3 and Mn3O4 on pristine graphene substrates. Both methods demonstrate the potential of depositing and transforming multifunctional oxides on single-crystal graphene using QEG substrates, allowing for the formation of nanostructured heterostructures previously unseen. Additionally, the electrochemical nature of the deposition presents the ability to scale the process to the QEG wafer and adjust the solution to produce other powerful multifunctional oxides.