This study investigated the role of Extracellular Polymeric Substances (EPS) extracted from waste activated sludge (WAS) and anaerobic granular sludge (AGS) on the reduction of selenite and tellurite. The tightly bound fraction of EPS (TB-EPS) from AGS gave the highest (>95%) removal efficiency of selenite and tellurite. The EPS reduced these oxyanions to their elemental forms as either selenium (Se) or tellurium (Te) nanoparticles (NPs) in mono metalloid incubations as well as conjugated (Se–Te) NPs for bi-metalloid incubations. The NPs were treated with two detergents and two enzymes to remove portions of the EPS coating of the NPs. The capping material was quantified along with the measurement of parameters such as size, surface charge and polydispersity. The smaller size (24.7–123 nm) and higher negative zeta-potential (−33.5 mV) of Se–Te NPs in conjugated form indicates more structural integrity compared to the Se and Te NPs in their individual form. The intermolecular interactions of proteins and extracellular DNA (eDNA) provided enhanced colloidal stability. This work revealed the previously unexplored roles of EPS in selenite and tellurite reduction and the features of the respective NPs in individual and conjugated form.