A new cream formulation containing hyaluronic acid 5%, complexed with a mix of a bacterial-wall-derived glycoprotein and peptide glycan complex (EDS), has been recently developed. We evaluated in a prospective, assessor-blinded, 6-week study the efficacy and tolerability of EDS in the treatment of facial seborrheic dermatitis (SD) and the effects on skin microbiota. Seventy-five subjects (mean age 46; 60 men) with moderate-severe SD of the face were enrolled. EDS cream was applied twice daily. The primary outcome was the evolution of the Investigator Global Assessment (IGA) score, evaluating erythema, scale/flaking, grade of seborrhea and itch. Superficial skin bacterial microbiome at baseline and after treatment was assessed, using the 16S rRNA gene methodology, in affected and non-affected face areas. Local tolerability was evaluated checking self-reported side effects at each visit. Baseline IGA scores (mean±SD) was 10±3. The use of EDS reduced IGA score significantly by 70% at week 3 and by 88% at week 6. An increase in the abundance of genera associated with a significant drop of genera presence was detected in affected areas. The ratio of relative abundance of genera Cutibacterium increased significantly after treatment in affected areas. The product was very well tolerated. Treatment with EDS applied twice daily for 6 consecutive weeks was associated with a reduction of the signs and symptoms of SD. Furthermore, after EDS cream treatment, a reequilibrating effect on facial skin microbiota was observed. The product was very well tolerated.