Skin microbiota, and its diversity and balance, play a key role in skin health and beauty, influencing skin moisture, barrier function, and radiance. A healthy skin microbiota limits the growth of detrimental species, protecting the skin from pathologies. Prebiotics can support beneficial populations in outcompeting detrimental ones. Dragon fruit (Hylocereus undatus) contains prebiotic polysaccharides effective on gut bacteria. Its extract was tested in vitro, in a coculture model including representative beneficial and detrimental species, and in double-blind, placebo-controlled clinical trials. Effects on the skin microbiota were measured via 16S rDNA sequencing, and skin health and beauty benefits were evaluated through image analysis, TEWL measurement, and chromametry. Doppler flowmetry measured skin resilience. The extract supported S. epidermidis and S. hominis (beneficial species), while limiting S. aureus and C. acnes (representing pathogens) in vitro. Clinical results demonstrated its beneficial effects on skin microbiota diversity, especially in older volunteers (Faith’s index up to +20% vs. placebo). Improvements were shown in skin sensitivity and resilience (by ca. 30% vs. placebo), skin redness (reflecting inflammation status), pigmentation and radiance (+11% ITA), barrier function (−13% TEWL), and wrinkling. This demonstrates this extract’s positive effects on the beauty, health, and microbiota balance of the skin.