The elemental composition and morphology of aerobic granules in sequencing batch reactors (GSBRs) treating high-nitrogen digester supernatant was investigated. The investigation particularly focused on the effect of the number of anoxic phases (one vs. two) in the cycle and the dose of external organics loading (450 mg COD/(L·cycle) vs. 540 mg COD/(L·cycle)) on granule characteristics. Granules in all reactors were formed of many single cells of rod and spherical bacteria. Addition of the second anoxic phase in the GSBR cycle resulted in enhanced settling properties of the granules of about 10.6% and at the same time decreased granule diameter of about 19.4%. The study showed that external organics loading was the deciding factor in the elemental composition of biomass. At 540 mg COD/(L·cycle) the granules contained more weight% of C, S and N, suggesting more volatile material in the granule structure. At lower organics loadings granules had the higher diameter of granules which limited the diffusion of oxygen and favored precipitation of mineral compounds in the granule interior. In this biomass higher content of Mg, P and Ca, was observed.