The impact of high-pressure processing (HPP) extraction on the structural, rheological, and functional properties of goji berry and raspberry pectic polysaccharides were investigated under acidic and alkaline conditions. These properties were compared with those of pectic polysaccharides extracted by conventional hot-acid and cold-alkali methods. Extraction yield, molecular weight, rheological behavior, and antioxidant activity of pectic extracts depended on the source materials of extraction. The solvent pH was the driving factor for the degree of esterification, as revealed by NMR and FTIR analysis. Monosaccharide composition was the primary variable between the extracts. The hot-acid extraction led to the highest galacturonic acid (GalA) contents, 46.9% for goji berry and 65.2% for raspberry, indicating the prevalence of homogalacturonans (HG) regions. HPP-assisted acidic/alkaline extractions gave rise to higher rhamnogalacturonan-I (RG-I) regions, pointing to the prevalence of hairy regions. The antioxidant activity of raspberry extracts was significantly (P ≤ 0.05) higher than goji berry extracts. The higher amount of RG-I may determine the higher antioxidant activity of raspberry pectic polysaccharides. The correlation between structural parameters and the lipase inhibitory activity also revealed that the higher lipase inhibitory activity of pectic polysaccharides is mostly correlated with the higher content of RG-I (r = 0.9259, P = 0.00033). Thus, HPP-assisted extraction may intensify the lipase inhibitory activity of pectic polysaccharides by increasing their RG-I content. Display omitted •Goji berry and raspberry pectins were obtained by high-pressure processing, hot-acid, cold-alkali.•Effects of extraction method on extracts yield, Mw and rheology were source-dependent.•Hot-acid extraction led to the highest galacturonic acid content (high HG region).•HPP-assisted extractions increased rhamnogalacturonan-I (RG-I) regions.•Higher RG-I is correlated with higher lipase inhibitory activity of pectin.