Anaerobic ammonium oxidation (anammox) is a cost-effective process to treat high-strength nitrogenous wastewater. Even without organic carbon input, the effluent contains bioproducts from autotrophic and heterotrophic bacteria. In this work, excitation–emission matrix (EEM) fluorescence spectroscopy was used to characterize the effluent dissolved organic matter (EfOM) from an anammox reactor treating synthetic wastewater. Two dominant EEM components were identified as humic acid-like (component 1) and protein-like (component 2) substances with excitation/emission peaks at <240, 355, 420/464 nm and <240, 280, 330/346 nm, respectively. The presence of both compounds in the effluent was tracked during an activity recovery period (nitrogen load increased from 0.2 to 1.3 kg N m−3 d−1). The effluent concentration of both components increased during this period, indicating correlation between production and bacterial activity. The dynamics of these bioproducts during both substrate consumption and starvation phases was analyzed in batch experiments. Component 1 was only formed during substrate consumption in a rate proportional to ammonium removal and was considered an up-take associated product characteristic of anammox activity. The results show that the composition of the EfOM was qualitatively and quantitatively influenced by process performance. Monitoring the EfOM could, therefore, offer a useful approach to assess anammox process performance and must be further explored.