The microbiota of Anopheles mosquitoes influences malaria transmission. Antibiotics ingested during a blood meal impact the mosquito microbiome and malaria transmission, with substantial differences between drugs. Here, we assessed if amoxicillin affects the mosquito microbiota . We collected Anopheles larvae in Burkina Faso, kept them in semi-field conditions and offered a blood meal to adult females. We tested the impact of blood supplementation with two alternative amoxicillin preparations on microbiota composition, determined by high-throughput sequencing in individual gut samples. Our mosquitoes harbored four main genera, Elizabethkingia, Wigglesworthia, Asaia and Serratia . The antibiotic treatment significantly affected overall microbiota composition, with a specific decrease in the relative abundance of Elizabethkingia and Asaia during blood digestion. Besides its interest on the influence of amoxicillin on the mosquito microbiota, our study proposes a thorough approach to report negative-control data of high-throughput sequencing studies on samples with a reduced microbial load.