It was assumed that, high purity endo-arabinanase and endo-mannanase could be useful in the isolation of pectin of enhanced health-promoting potential. Extraction was carried out with 50 U of enzymes per gram of apple pomace at 40 °C, obtaining up to 22% increase in effectiveness, as compared to the acid extraction. The pectins, despite their high Mw, were homogeneous and contained more galacturonic acid, rhamnose, galactose, fucose, and ferulic acid than the conventional product, thanks to which they quenched free radicals up to five times more efficiently. Compared with pectin with recognised anticancer and prebiotic activity, they had a significantly greater ability to inhibit proliferation and migration of HT-29 and B16F10 cells. They were also more effective in preventing the adhesion of E. coli and S. typhimurium to enterocytes. Endo-arabinanase- and endo-mannanase-assisted extraction is an effective method of obtaining pectins with enhanced antiradical, anticancer and prebiotic potential.