The relationship between ammonia oxidation rate, nitrifiers population, and modelled aerobic zone volume in different granule sizes was investigated using aerobic granular sludge from a pilot-scale reactor. The pilot was fed with centrate and secondary effluent amended with acetate as the main carbon source. The maximum specific ammonia oxidation rates and community composition of different aerobic granular sludge size fractions were evaluated by batch tests, quantitative PCR, and genomic analysis. Small (331µm) granules had a 4.72 ± 0.09 times higher maximum specific ammonia oxidizing rate per 1 gVSS, and a 4.05 ± 0.17 times higher specific amoA gene copy number than large (2225µm) granules per 1 gram of wet biomass. However, when related to surface area, small granules had 1.43 ± 0.01 times lower maximum specific ammonia oxidation rate and a 1.66 ± 0.04 times lower specific amoA gene copy number per unit surface than large granules. Experimental results aligned with modeling results in which smaller granules had a higher specific aerobic zone volume to biomass and lower specific aerobic zone volume to surface area. Aerobic granular sludge reactors having the same average diameter of granules may have very different proportions of granule size fractions and hence possess different nitrification rates. Therefore, instead of the commonly reported average granule diameter, a new method was proposed to determine the aerobic volume density per sample, which correlated well with the nitrification rate. This work provides a roadmap to control nitrification capacity by two methods: (a) crushing larger granules into smaller fractions, or (b) increasing the mixed liquor suspended solid concentration to increase the total aerobic zone volume of the system.