A partial nitritation continuous flow reactor (CFR) was operated for eight months demonstrating that partial nitritation granular sludge can remain stable under continuous flow conditions. The ammonia oxidizing bacteria (AOB)-to-nitrite oxidizing bacteria (NOB) activity ratios were determined for a series of granule sizes to understand the impact of mass diffusion limitation on the free ammonia (FA) inhibition of NOB. When dissolved oxygen (DO) limitation is the only mechanism for NOB suppression, the AOB:NOB ratio was usually found to increase with the granule size. However, the trend is reversed when FA has an inhibitory effect on NOB, as was observed in this study. The decrease in AOB:NOB ratio indicates that smaller granules, e.g. diameter < 150 mu m are preferred for nitrite accumulation when high FA concentration is present, as in the partial nitritation process. The trend was further verified by observing the increase in the apparent inhibition coefficient as granule size increased. Indeed, this study for the first time quantified the effect of diffusion limitation on the apparent inhibition coefficient of NOB in aerobic granules. A mathematical model was then utilized to interpret the observed suppression of NOB and predicted that NOB suppression was only complete at the granule surface. The NOB that did survive in larger granules was forced to dwell within the granule interior, where the AOB growth declines due to DO diffusion limitation. This means FA inhibition can be taken advantage of as an effective means for NOB suppression in small granules or thin biofilms. Further, both FA inhibition and DO limitation were found to be required for the suppression of NOB in mainstream aerobic granules.