Pomace is a residue of juice production, but still holds many valuable compounds, such as antioxidants. However, efficient extraction proves to be challenging, as extractability is highly dependent on experimental conditions. Furthermore, antioxidants are also often retained by structural polysaccharides. Consequently, this study investigates the extractability of antioxidants in five different types of pomace in a 2 × 2 × 2 × 3 full factorial fully replicated design to determine the most efficient way of extraction. Therefore, extracting agent, temperature, extraction method and use of enzyme to break down structural components were alternated to investigate the effects of these parameters on the extractability. Main effects as well as interaction effects were estimated with linear mixed models. To study the effects of polysaccharides on the retention of antioxidants, the amount of soluble polysaccharides was measured and connected to the antioxidant capacity at each experimental condition. The experiments showed that acetone was most suitable as an extracting agent and that the use of pectinase significantly increased the amount of extracted antioxidants. Additionally, ultrasound-assisted extraction is advantageous compared to extraction in water bath. Temperature showed the lowest effect in this experimental design. Lastly, the results also highlight that the amount of soluble polysaccharides does not correlate with the extractability of antioxidants.