An accurate measurement of the bonding energy of an interface is important in many areas of applied research. We present a novel method for measuring the bonding energy, which is based on the principle of non-planar direct bonding, i.e., direct bonding of originally planar wafers onto non-planar substrates. We discuss in detail the advantages and disadvantages compared to the commonly used double cantilever beam method. To demonstrate the practical relevance, by using the example of glass wafers, the evolution of the bonding energy during different de-bonding steps is investigated, focusing on how the surface shape variations and the surface roughness affects water stress corrosion. We find that the bonding energy in the corroded state is not affected by the original surface shape variations and mid-spatial frequency range roughness, anymore. A molecular mechanism to explain this phenomenon is proposed.