(1) Background: The dysbiosis of some cutaneous commensal microorganisms is the trigger factor for the activation of the inflammatory cascade by keratinocytes in many skin disorders. Mesotherapy is an innovative technique for many scalp disorders, with the function of restoring the physiology of the skin. (2) Methods: the antimicrobial, antibiofilm and anti-inflammatory activity of the non-cross-linked HA formulation (Hydro Deluxe, Matex Lab S.p.a., Brindisi, Italy) was investigated against the most common microorganisms of the scalp (Staphyloccoccus epidermis, Staphyloccoccus aureus, Cutibacterium acnes and Malassezia furfur). Anti-inflammatory activity was evaluated on an internal 3D model of Reconstructed Human Epidermis (RHE) inserts infected with the strains as pro-inflammatory stimulus. (3) Results and Conclusions: the data collected showed a good antimicrobial and antibiofilm activity against all selected strains. The HA-based formulation did not show cytotoxicity on RHE, either alone or in presence of the infectious stimulus. The analysis of the expression of Interleukin (IL)-8 levels showed an excellent ability to reduce this pro-inflammatory marker. Overall, the efficacy assessment of the formulation supported its potential effectiveness in mesotherapy for the treatment of scalp disorders.