To date, the partial nitrification-Anammox (PN-A) granular sludge size has been exclusively analyzed in synthetic substrates. In this work, different ranges of granular size of PN-A sludge were studied at low oxygen concentration using real industrial wastewater as, well as a synthetic substrate. The granular sludge was characterized by the specific nitrification activity (SNA), specific anammox activity (SAA), and granule sedimentation rate. The relative abundance of the bacterial consortium was assessed for each range of diameters through the fluorescence in situ hybridization (FISH) technique. SNA exhibits a direct association with the specific surface of granules, which proves the importance of the outer layer in the nitrification process. Even more critical, the flocculent sludge allowed the stability of the nitrifying activity. The SAA showed different performances faced the real industrial and synthetic substrates. With the synthetic substrate, the SAA decreased at higher diameter ranges, whereas with the industrial substrate, the SAA increased at higher diameter ranges. This situation is explained by the oxygen protection in the sludge maintained with industrial wastewater. The relative abundance of heterotrophic bacteria increased from 9.6 to 22%, due to the presence of organic matter in the industrial substrate. The granular sedimentation rate increased with the diameter of the granules with a linear correlation (R2 > 0.98). Thus, granular sizes can be selected through sedimentation rate control. A linear correlation between SAA and granular sludge diameter ranges was observed. With this correlation, an error of less than 11% in the prediction of SAA was achieved. The use of diameter measurement and granular sedimentation rate as routine techniques could contribute to the control and start-up of PN-A reactors. In the same sense, organic matter present in defined concentrations, can be beneficial for the granular sludge stability, and thus, for nitrogen removal.