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Abstract The human skin microbiota plays a key role in the maintenance of healthy skin, ensuring protection and biological barrier by competing with pathogens and by closely communicating with the immune system. The development of approaches which preserve or restore the skin microbiota represents a novel target for skincare applications. Prebiotics could be applied to balance almost any microbial community to achieve advantageous effects. However, information about their effectiveness as skin microbiota modulators is limited. The objective of the current study was to evaluate the effects of short chain fructo-oligosaccharides (scFOS) from sugar beet (DP 3–5), well-recognised prebiotics, on some representative bacterial strains of the skin microbiota. We measured the growth and competitive activity of these specific bacteria for the use of scFOS as energy source in minimal medium and in a reconstructed human epithelium (RHE) in vitro model. In minimal growth medium, scFOS promoted and sustained the growth of Staphylococcus epidermidis up to 24 h, considered a beneficial skin commensal bacterium, while inhibiting both Cutibacterium acnes and Staphylococcus aureus growth, regarded as opportunistic pathogens. S. epidermidis showed the highest colonization potential and 1% scFOS was effective in shifting the competition in favour of S. epidermidis with respect to C. acnes in the RHE model. This latter effect was observed following 24 h of exposure, suggesting a long-term effect of scFOS in a highly skin dynamic environment. Therefore, scFOS could be effectively implemented in skincare formulations for recovering skin microbiota homeostasis.