Electrodeposition is a useful route to nanoparticle formation that allows control over nucleation and growth by tuning the applied potential. Here, electrodeposition is used to create Au structures on highly oriented pyrolytic graphite and monolayer graphene electrodes. It is demonstrated that spontaneous formation of Au occurs immediately on exposure to the solution, which strongly impacts the cyclic voltammetry and obfuscates the underlying deposition mechanism. Voltammetric measurements are combined with ex situ and in situ electrochemical atomic force microscopy to reveal the processes corresponding to Au deposition and stripping. Deposition on spontaneously formed Au dominates the voltammetry, with the deposition on clean areas of the electrode requiring a much greater overpotential. Additionally, comparison of the extent of deposition and the potentials required for different grades of graphite and monolayer graphene are found to be linked to the density of defects of the electrode. Consideration of such factors is important for obtaining small, highly uniform functionalisation of graphene-based materials suitable for applications.