The inhibitory effect of seven different metals on the specific anammox activity of granular biomass, collected from a single stage partial nitritation/anammox reactor, was evaluated. The concentration of each metal that led to a 50% inhibition concentration (IC50) was 19.3 mg Cu+2/L, 26.9 mg Cr+2/L, 45.6 mg Pb+2/L, 59.1 mg Zn+2/L, 69.2 mg Ni+2/L, 174.6 mg Cd+2/L, and 175.8 mg Mn+2/L. In experiments performed with granules mechanically disintegrated (flocculent-like sludge), the IC50 for Cd+2 corresponded to a concentration of 93.1 mg Cd+2/L. These results indicate that the granular structure might act as a physical barrier to protect anammox bacteria from toxics. Furthermore, the presence of an external layer of ammonia oxidizing bacteria seems to mitigate the inhibitory effect of the metals, as the values of IC50 obtained in this study for anammox activity were higher than those previously reported for anammox granules. Additionally, the results obtained confirmed that copper is one of the most inhibitory metals for anammox activity and revealed that chromium, scarcely studied yet, has a similar potential inhibitory effect.