Introduction: Microorganisms as a component of scalp ecosystem play a vital role in human scalp health. Soapberry pericarp is employed in improving scalp health, and its content of active ingredients could be enhanced resulted in fermentation. This study aims to investigate the effect of the fermentation filtrate from soapberry pericarp on the diversity of scalp microorganisms., Methods: The components in fermentation filtrate from soapberry pericarp were analyzed by HPLC-Q-Orbitrap HRMS, and 16S and ITS sequences of 198 samples from three different used stages (Day 0, Day 7, Day 28) were sequenced using the Illumina Novaseq platform. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (weighted unifrac and unweighted unifrac). Principal coordinate analysis (PCoA) and linear discriminant analysis (LDA) effect size analysis (LEfSe) were used to visualize microbial variation among different stages., Results: There were 22 components were identified in the fermentation filtrate from soapberry pericarp by HPLC-Q-Orbitrap HRMS. The alpha-diversity and beta-diversity analyses showed that scalp microbial diversity and composition were influenced by the fermentation filtrate of soapberry pericarp. Based on functional analysis, this study found an enrichment of healthy scalp-related bacterial pathways, such as amino acid, nucleoside, and nucleotide biosynthesis, while a decrease in fungal pathogenesis pathways, specifically saprotroph and symbiotroph pathways, was observed., Discussion: The study described about the complex community dynamics of human scalp microorganisms during the stages of using the fermentation filtrate from soapberry pericarp. This result will help rationally utilize the fermentation filtrate from soapberry pericarp to keep or improve human scalp health., Competing Interests: CX, DP, DZ, LL, YC, and JH were employed by Guangzhou Uniasia Cosmetics Technology Co., Ltd. The remaining author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Xu, Pan, Zhang, Lin, Chen, Liang and He.)