The concentration and N2O production and consumption rates in an aquaponic system (fish tank, settling tank, and biofilter) were quantified during a culture cycle to determine if this type of system contributes to the emission of N2O and the microbial communities involved. Chemical inhibition (allylthiourea and acetylene) and metataxonomic techniques were applied. The results indicated that the highest dissolved N2O concentrations were recorded in the biofilter (1.99±0.74 µM), and a net N2O production rate was observed in all the compartments, reaching the highest value (324.4 nM d-1) in the settling tank. The N2O production was associated with nitrification (rates up to 168.6 nM d-1) and denitrification (rates up to 372±180 nM d-1). Nitrification was predominantly related to ammonia-oxidizing bacteria and archaea. However, Comammox bacteria were present in the three compartments. Alphaproteobacteria, Bacteroidota, and Actinobacteria were the most abundant phyla shared between containers, including some genera reported as denitrifiers capable of producing N2O.