In the present study, the effect of microwave-assisted extraction conditions on the simultaneous recovery of pectin and phenolic compounds from sour cherry pomace (SCP) was optimized. The results showed that maximum yield of pectin (14.65 ± 0.39%) and phenolic compounds (14.36 ± 0.29%) was obtained under microwave power of 800 W, irradiation time of 300 s, pH of 1.00 and LSR of 20 v/w. The resulting pectin under the mentioned conditions had the moisture, ash and protein content, and also total carbohydrates of ~8.32, ~3.73, ~1.41 and ~26.43%, respectively. Also, the obtained pectin with the molecular weight of 472.977 kDa and total phenol content of 91.54 ± 2.92 mg GAE/g pectin had a high purity (galacturonic acid content of ~72.86%) and suitable thermal stability (degradation temperature of 252.15 °C) and also could be classified as HMP (DE of 68.37 ± 2.78%). The FTIR, 1H NMR and XRD analysis indicated that the obtained sample was rich in esterified poly-galacturonic acid and had an amorphous structure. The phenolic compounds analysis showed that the SCP extract had a concentration-dependent antioxidant effect that was comparable with ascorbic acid and BHA at high concentrations.