A classification of gluten polymer networks would support a better understanding of structure-function relationships of any gluten polymer material and thus, the control of processing properties. However, quantification and interpretation of the gluten network structures is challenging due to their complexity. Thus, the network formation was altered by specific gluten-modifying agents (glutathione, ascorbic acid, potassium bromate, glucose oxidase, transglutaminase, bromelain) in this study in order to clarify if structural alterations can be detected on a microstructural level and to specify different polymer arrangements in general. Microstructure analysis was performed by confocal laser scanning microscopy followed by quantification with protein network analysis. It was shown that alterations in gluten microstructure could be elucidated according to the kind of modification in cross-linking (disulphide, (iso) peptide, dityrosyl). Linear correlations of structural network attributes among each other were found, leading to an assertion in general: the higher the branching rate, the thinner the protein threads and the larger the interconnected protein aggregate. Considering the morphological attribute lacunarity, a quantitative classification of different gluten arrangements was established. These assertions were extended by using unspecific gluten-modifying agents in addition to the specific ones. Ultimately, five network types were proposed based on diverse polymer arrangements.