Methods for compensating for warp typically exhibited by glass-based articles having non-uniform thicknesses as a result of ion exchange strengthening are provided. The methods include producing a molding surface of a mold based on a measurement of warp obtained by a specified ion exchange strengthening of a glass-based substrate of non-uniform thickness, such that the molding surface offsets the warp. Glass-based substrates resulting from the mold can then be exposed to the specified ion exchange strengthening and form glass-based articles that are substantially free of warp.