A holistic approach was developed towards efficient bacterial resource management for nutrient removal from wastewater in aerobic granular sludge sequencing batch reactors. Multiple reactor experiments from granulation start-up to operation at steady-state were conducted in order to understand the mechanisms of bacterial selection by identification of multilevel correlations from reactor to biofilm and microbial scales. A stable, cooperative, and active Accumulibacter-dominated bacterial community continuum is selected by proper control of the anaerobic contact time, starvation phase length, and sludge age by taking advantage of the flexibility of the SBR technology. Microenvironmental conditions such as pH (>7.25), temperature (<20°C), nutrient composition (>30 gCOD gP-1 and >10 gCOD gN-1), and the presence of propionate in the influent wastewater can in addition lead to a robust bioprocess.