Food by-products can be used as natural and sustainable food ingredients. However, a modification is needed to improve the technofunctional properties according to the specific needs of designated applications. A lab-scale twin-screw extruder was used to process enzymatically treated apple pomace from commercial fruit juice production. To vary the range of the thermomechanical treatment, various screw speeds (200, 600, 1000 min−1), and screw configurations were applied to the raw material. Detailed chemical and functional analyses were performed to develop a comprehensive understanding of the impact of the extrusion processing on apple pomace composition and technofunctional properties as well as structures of individual polymers. Extrusion at moderate thermomechanical conditions increased the water absorption, swelling, and viscosity of the material. An increase in thermomechanical stress resulted in a higher water solubility index, but negatively affected the water absorption index, viscosity, and swelling. Scanning electron microscopy showed an extrusion-processing-related disruption of the cell wall. Dietary fiber analysis revealed an increase of soluble dietary fiber from 12.6 to 17.2 g/100 g dry matter at maximum thermo-mechanical treatment. Dietary fiber polysaccharide analysis demonstrated compositional changes, mainly in the insoluble dietary fiber fraction. In short, pectin polysaccharides seem to be susceptible to thermo-mechanical stress, especially arabinans as neutral side chains of rhamnogalacturonan I.