Seborrheic dermatitis (SD) is a current skin disorder, touching 1-3% of the population, characterized by presence of inflammatory areas in the scalp and itching. It is associated with high level of sebum production and presence of dandruffs. The role of the Malassezia yeast in the exacerbation of SD has been clearly established, acting through their high lipase activity. For this reason, anti-fungal shampoos are paramount in the treatment of SD. The high Malassezia colonization in SD induces modification of the skin composition. Hence, skin metabolomics is key approach for better understanding this skin inflammatory disorder and the molecular mechanisms induced by the antifungal treatment. Metabolomic analyses are usually performed by LC-MS approach which require delicate sample preparation as well as several separative conditions. In the present study, we wanted to evaluate the potential of an innovative MS approach, the SpiderMass. Interestingly, the SpiderMass analysis were performed from cigarette papers simply rubbed over the skin that were directly analyzed without further sample preparation. Patients were analyzed before and during the treatment with a novel antifungal agent at different time points to monitor the changes in the skin composition. The statistical analysis revealed that many molecules were modulated by the treatment. Changes in the abundance of different molecules, more specifically, a strong change in the lipid profile of the scalp was observed, with a reduction in markers of inflammation and pruritus as well as a return to a healthy balance of glycerolipids and free fatty acids was identified. A clear restoration of lipids profiles during the treatment with the anti-fungal shampoo was achieved. Thus, SpiderMass appears as a perfectly adapted technique for clinical evaluation of skin pathologies especially considering that the technology can be conducted in vivo and in real-time.