This study investigated the inhibitory effect of three antibiotics: oxytetracycline (OTC), ciprofloxacin (CIP), and clarithromycin (CLA) on the anammox process conducted in four sequencing batch reactors (SBRs). The concentration of each antibiotic was 0.001 mg L−1, similar to concentrations observed in municipal wastewater treatment plants. The specific anammox activity (SAA) of the anammox process was measured using a batch test, the microbial community structure was analyzed using high-throughput sequencing, and the variation of functional genes and antibiotic resistance genes (ARGs) abundance were measured by qPCR. These results indicated that none of the antibiotics significantly impacted nitrogen removal rate (NRR) in the anammox process and specific anammox activity (SAA). Analysis of the functional gene abundance variation showed significant inhibition of hzo by antibiotics while in control and increased from 3.88 × 10−6 to 1.26 × 10−5. The relative abundance of almost all detected ARGs increased (tetC and tetW targeted OTC, qnrB4 and qnrS targeted CIP). Only two ARGs (tetX targeted OTC and mphA targeted CLA) decreased (from 1.62 × 10−2 and 7.45 × 10−3 to 3.74 × 10−4 and 9.3 × 10−5, respectively). Metataxonomic analysis showed a decrease in the relative abundance of anammox bacteria genera (Candidatus Brocadia, Candidatus Jettenia) in each tested reactor, and a significant increase of Nitrospira, regarded as a comammox microorganism. The purpose of this study was to evaluate the effect of trace concentration of three commonly detected antibiotics (OTC, CIP, CLA) in wastewater on the anammox process. Furthermore, CIP and CLA have never been investigated relative to the anammox process.