Atopic dermatitis (AD) is a widespread chronic inflammatory dermatologic disorder. This randomized, double-blind study aims to evaluate the effect of synbiotic baths with a defined mixture of six viable lactic acid bacteria (LAB) and prebiotics, without bacteria and prebiotics and placebo baths without prebiotics and bacteria to treat AD patients over a period of 14 days. Therefore, AD patients were randomly assigned into three groups using synbiotic (n = 7), prebiotics (n = 8) or placebo baths (n = 7). Severity of AD was evaluated over time by using severity scoring of atopic dermatitis (SCORAD) and by patient questionnaires. In addition, microbiome on eczematous skin surface was sampled by swaps from each patient before the bath treatment, and after 9, 11 and 14 days of bath treatment. Thereafter, nucleic acids were extracted and the bacterial 16S rRNA gene was amplified via PCR for subsequent amplicon sequencing. Results showed a significantly reduced SCORAD over time of AD patients after daily synbiotic or prebiotic baths. Moreover, AD patients after daily synbiotic baths had a significantly improved pruritus and skin dryness and their bacterial microbiome was enriched by LAB. Taken together, a synbiotic bath is a promising topical skin application to alleviate AD.