The ability of Anopheles mosquitoes to transmit malaria is significantly influenced by their gut microbiota. Antibiotics ingested during a blood meal impact the mosquito gut microbiome and influence malaria transmission. Such effects on the mosquito microbiota have been investigated for several antibiotics, but not for amoxicillin, one of the most frequently-used drugs. In this study, we assessed its effect on microbiota composition in the mosquito gut. We collected larvae of Anopheles coluzzii, An. gambiae and An. arabiensis from different sites in Burkina Faso and kept them in semi-field conditions until adulthood. We analyzed by high-throughput sequencing the gut microbiota composition in individual females fed on the blood of a Plasmodium-naïve donor and of two gametocyte-carriers. In each experiment, we tested the impact of blood supplementation with amoxicillin or a cocktail of amoxicillin and clavulanic acid.We identified four dominant genera in mosquitoes from Burkina Faso, notably namely Serratia, Asaia, Elizabethkingia and Wigglesworthia. In antibiotic-free samples, Elizabethkingia and Asaia had a significantly higher relative abundance in mosquitoes having ingested blood from Plasmodium gametocyte-carriers. This observation may be linked to the presence of gametocytes or to variations between donors and/or replicates. Antibiotic treatment significantly decreased the proportion of Elizabethkingia, Asaia and Comamonas in the gut microbiota 24 h after the blood meal. Besides its interest on the influence of amoxicillin on the mosquito microbiota, our study proposes a thorough approach to present data from negative controls when reporting data from samples with a reduced microbial load.