A multi-scale computational model was created for the formation of activated sludge floc structure. The model couples mass balances for substrates and biomass at reactor scale with an individual-based approach for the floc morphology, shape and microcolony development. Among the novel model processes included are the group attachment of micro-flocs to the core structure and the clustering of nitrifiers. Simulation results qualitatively describe the formation of globular colonies of ammonia and nitrite oxidizers in the extracellular polymeric substance produced by heterotrophic microorganisms, as also observed in fluorescence in situ hybridization images. These results are the first step towards a multi-scale model of the activated sludge wastewater treatment systems, which could also be extended to other engineered biological systems.