Acid and its formation and placement is one of the most important aspects in the chemically amplified photolithographic process. The choice of photoacid generator (PAG) in the photolithographic patterning of acidic substrates, such as PEDOT:PSS, has consequences for the resolution and overall quality of the patterned image. In this study, an acid exchange and diffusion mechanism is proposed for the undesired decomposition of the unexposed photoresist layer containing ionic PAGs. The use of non-ionic PAGs has been shown to be a solution to this decomposition problem. In addition, the acidic nature of the PEDOT:PSS substrate is employed to produce patterned images of a cross-linkable light-emitting polymer. With further optimization and development, this is potentially a fast and simple method to introduce patterns in various organic electronic devices.