Fouling distinctly reduces the filtration performance of membranes. A characterization of the fouling in membranes, however, is difficult due to its spatial distribution. Currently applied methods for deposit layer analysis are rather complex or do not offer a spatial resolution. Knowledge of the spatial distribution, however, could be used to improve the design of membranes, modules, and spacers. Staining with Coomassie Brilliant Blue, related to the staining of PAGE gels, is a simple method to visualize and analyze the deposited proteins semi-quantitatively. We improved an existing staining technique for protein deposits on membranes by adding a calibration for the semi-quantitative analysis and optimizing the sample handling. The method provides a spatially resolved analysis of deposited proteins up to a concentration of 10 g m−2. Apart from staining, data processing is described in order to generate false colors or topographic images of deposits. Thus, the paper describes a simple method to assess and visualize the influence of module characteristics such as spacer design on the spatially resolved protein fouling of polymeric and ceramic membranes. Therefore, the method can contribute to the improvement of the module design and processing conditions with regard to the filtration performance.•Visualization of proteinaceous deposits on membranes•Spatially resolved quantification of proteinaceous deposits