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Most of nitrogen emissions can be ascribed to agro-industrial activities. Since digestate produced by fermentation of agro-industrial residues can be difficult to dispose of due to its high ammonium content, advanced technical- and cost-effective technologies must be developed and applied in order to significantly reduce its impact on the environment. In this study, aerobic granules were successfully cultivated in a granular sludge sequencing batch reactor (GSBR) fed with the ammonium-rich (approx. 2500 mg L−1) effluent of a 3-stage anaerobic digester treating agro-industrial residues. The peculiar characteristics of such wastewater required a 2-step operating strategy aimed at the selection of nitrifying biomass (Step 1) and the formation of aerobic granular sludge (Step 2). During Step 1, nitrifying biomass selection was achieved by properly regulating the cycle length: N H 4 + - N removal rates progressively increased from 42 to 109 mgN L−1d−1, and a corresponding increase in N H 4 + - N specific removal rates from 8 to 24 mgN gVSS−1d−1 was also observed. During Step 2, the increase in selective pressures (i.e. minimum settling velocity and volumetric organic loading rate) led to the formation of compact (average diameter, 1.02 ± 0.43 mm) and well-settling granules (SVI5, 28.6 ± 3.8 mL gTSS−1), which were able to remove up to 89 ± 2% of organic matter (as COD), 79 ± 3% of N H 4 + - N and 59 ± 4% of nitrogen (as a sum of N H 4 + - N , N O 2 – - N and N O 3 – - N ). The 2-step operating strategy played a key role in biomass selection and subsequent granule formation and maintenance in the GSBR, and may be successfully adopted for the treatment of different ammonium-rich wastewaters. [ABSTRACT FROM AUTHOR]