Background:Mass deworming programs using anthelmintic drugs are a common public health strategy for controlling soil-transmitted helminth (STH) infections in high-risk, low-income countries. However, whether routine deworming induces long-term changes in gut microbiome composition remains unclear. We used longitudinal data to examine how anthelmintics alter the gut microbiome profiles of Ethiopian children. Methods: Fecal samples were collected from school-aged children enrolled in a mass deworming program in Jimma, Ethiopia, before and after receiving a 400 mg dose of albendazole. Baseline samples were collected from 132 participants between April and May 2020, prior to treatment. Follow-up samples were obtained one year later from 67 children who remained in the study. Results:We observed a significant change in gut microbiome diversity metrics one year following treatment, characterized by fewer observed taxa and increased community evenness (Shannon and Simpson indices, p < 0.01), indicating substantial perturbation of microbial community structure. Furthermore, we identified six significantly enriched genera post-treatment (FDR-adjusted p < 0.05) among participants who were helminth-negative at the baseline, including Blautia, Senegalimassilia, Coprococcus 1, Marvinbryantia, Clostridium sensu stricto 1, and Lachnospiraceae ND3007 group. In contrast, individuals who had at least one egg count of Ascaris lumbricoides, Trichuris trichiura, or hookworm before treatment exhibited enrichment in five taxa (Senegalimassilia, Lachnospiraceae ND3007 group, Lachnospiraceae FCS020 group, Collinsella, and Intestinimonas). Conclusions: Our findings suggest that baseline helminth infection status influences the microbiome changes induced by anthelmintic treatment. Further controlled animal studies are needed to clarify how anthelmintic treatment affects taxon shifts in gut microbiota.