The final characteristics of plant protein-based high moisture extrudates depend on the processing conditions and the composition of the raw materials. In this study, different soy protein-based formulations containing zein and rice starch were studied for the development of plant-based gluten-free high moisture extrudates. The physicochemical, rheological, textural, and microstructural characteristics of the final products were studied and related to the product formulation and the secondary structure of the participating proteins. Changes in the type and concentration of proteins had significant effects on the final rheological and microstructural properties of the resulting products, but these were not directly associated to changes on the secondary structure of proteins. The addition of rice starch generated softer products, while proteins' molecular associations and conformational arrangements defined the textural and microstructural characteristics. Products prepared with gluten (control) generated a layered and fibrous structure, but the study showed that gluten-free products with similar microstructural characteristics could be obtained from the addition of zein and rice starch. These results confirmed the key role of the formulation on the definition of the final characteristics of gluten-free products and that zein can be used for the generation of plant protein-based high moisture extrudates with desired textural properties.