The valorization of by-products eliminates the risks of economic barriers and reduces the overall amount of pollution and the carbon footprint of the products. In this context, conventional heating extraction (CE) and microwave-assisted extraction (MAE) were compared to extract pectin from apple pomace. The effects of temperature on MAE were evaluated based on the resulting properties obtained in subsequent pectin hydrogels. A pectin yield of 10.6 ± 0.3% was obtained by MAE with 5 min extraction, while CE showed a yield of 9.5 ± 0.3% after 2 h. The pectin extracted by both methods had a low methoxyl content, indicating a low degree of esterification. The galacturonic acid content was greater than 60% for most samples. Zeta potential analysis indicated the ability of the pectin to form stable gels. According to the X-ray diffractograms, increasing the extraction temperature led to a decrease in the crystallinity of the pectin structure. Rheological tests showed increased storage modulus as the temperature increased by MAE from 80 to 100 °C for the pectin-based hydrogel. The water holding capacity was greater than 50% for all hydrogels. Furthermore, an analysis of electrical consumption and energy costs highlighted the economic advantage of using microwave heating technology to extract pectin.