Blackcurrant pomace is a widely available waste stream derived from the industrial production of juice rich in pectin and unextracted polyphenols. Since pectin, an emerging class of gastrointestinal prebiotics, is also a common cosmetic ingredient, the aim of this work was to evaluate blackcurrant pomace as a source of pectin-rich fractions suitable for application in prebiotic cosmetics. Hereby, this raw material was valorised by sequential extraction of acid-soluble (by citric acid, CAP) and Ca-bound (by ammonium oxalate, AOPP) pectic polysaccharides. Both fractions had favourable physicochemical features and a similar degree of methyl-esterification between low- and high-methoxyl pectin (approx. 50%), but CAP had significantly higher galacturonic acid content (72.3%), branching, and purity. Regardless of that, both had very high oil (18.96 mL/g for CAP and 19.32 mL/g for AOPP) and water (9.97 mL/g for CAP and 7.32 mL/g for AOPP)-holding capacities and excellent emulsifying properties, making them promising cosmetic ingredients. The polyphenol content was 10 times higher in CAP, while corresponding antioxidant activity was 3-fold higher. Finally, the influence of varying CAP and AOPP concentrations on common skin pathogen, Staphylococcus aureus, and beneficial skin bacteria, Staphylococcus epidermidis, was examined. The results show significant prebiotic potential of two pectic fractions since they were capable of selectively stimulating S. epidermidis, while S. aureus growth was inhibited, whereas CAP demonstrated a particularly high capacity of up to 2.2, even with methicillin-resistant S. aureus.