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Seborrheic dermatitis (SD) is the most prevalent dermatological disease, occurring in up to 50% of the population around the world. The antimicrobial resistance of SD-related microflora contributed to the research of novel substances. Thus, the aim of the study was the development of the novel terpene-enriched plant-based combination and research its antimicrobial potential against standard microorganisms involved in the pathogenesis of SD. Through DiffDock computational modelling to predict affinity for microbial H+-ATP synthase and biological activity, Melaleuca alternifolia leaf oil (TTO), 1,8-cineole, and α-(-)-bisabolol were chosen. Moreover, the combination of TTO, 1,8-cineole and α-(-)-bisabolol in a 1:1:1 mass ratio was analyzed by gas chromatography–mass spectrometry (GC-MS). Staphylococcus epidermidis ATCC 14990, Staphylococcus aureus ATCC 29213, Micrococcus luteus ATCC 10240a, Candida albicans ATCC 10231, Malassezia furfur ATCC 14251 were used for antimicrobial assays to determine the MICs by broth microdilution method. Finally, the combination’s ability to inhibit Malassezia furfur as the main pathogen involved in the pathogenesis of SD was evaluated. Based on GC/MS assay, eighteen compounds were identified with prevalence of (-)-α-bisabolol (25.73%), 1,8-cineole (22.28%) and terpinen-4-ol (20.88%). The results showed that the combination based on TTO, 1,8-cineole and α-(-)-bisabolol in a 1:1:1 mass ratio has a clear synergistic antimicrobial and antifungal activity against scalp commensal bacteria related to SD. The substance showed a MIC value of 1.25 mg/mL against Staphylococcus epidermidis and Staphylococcus aureus, while scalp-friendly Micrococcus luteus was not sensitive. The plant-based combination demonstrated a pronounced antifungal effect against fungi, with a MIC of 5.00 and 2.50 mg/mL against Malassezia furfur and Candida albicans respectively. The combination had a decrease in more than 2log10CFU of Malassezia furfur, corresponding to >99% antifungal activity after 1 h of contact in comparison with climbazole- and ketoconazole-mediated effect. It can be concluded that the novel terpene-enriched plant-based combination has a promising targeted antimicrobial potential for the treatment of SD.