Background Atopic eczema (atopic dermatitis, AD) is characterized by disrupted skin barrier associated with elevated skin pH and skin microbiome dysbiosis, due to highStaphylococcus aureusloads, especially during flares. SinceS aureusshows optimal growth at neutral pH, we investigated the longitudinal interplay between these factors and AD severity in a pilot study. Method Emollient (with either basic pH 8.5 or pH 5.5) was applied double-blinded twice daily to 6 AD patients and 6 healthy (HE) controls for 8 weeks. Weekly, skin swabs for microbiome analysis (deep sequencing) were taken, AD severity was assessed, and skin physiology (pH, hydration, transepidermal water loss) was measured. Results Physiological, microbiome, and clinical results were not robustly related to the pH of applied emollient. In contrast to longitudinally stable microbiome in HE,S aureusfrequency significantly increased in AD over 8 weeks. HighS aureusabundance was associated with skin pH 5.7-6.2. High baselineS aureusfrequency predicted both increase inS aureusand in AD severity (EASI and local SCORAD) after 8 weeks. Conclusion Skin pH is tightly regulated by intrinsic factors and limits the abundance ofS aureus. High baselineS aureusabundance in turn predicts an increase in AD severity over the study period. This underlines the importance and potential of sustained intervention regarding the skin pH and urges for larger studies linking skin pH and skinS aureusabundance to understand driving factors of disease progression.