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Abstract The economic factor of the microalgae harvesting step acts as a barrier to scaling up microalgae-based technology designed for wastewater treatment. In view of that, this study presents an alternative microalgae-bacteria system, which is proposed for eliminating the economic obstacle. Instead of the microalgae-bacteria (activated algae) flocs, the study aimed to develop activated algae granules comprising the microalgae Chlorella sp. as a target species. The presence of the filamentous microalgae (Phormidium sp.) was necessary for the occurrence of the granulation processes. A progressive decrease in frequency of the free Chlorella sp. cells was achieved once with the development of the activated algae granules as a result of the target microalgae being captured in the dense and tangled network of filaments. The mature activated algae granules ranged between 600 and 2,000 µm, and were characterized by a compact structure and significant settling ability (21.6 ± 0.9 m/h). In relation to the main aim of this study, a microalgae recovery efficiency of higher than 99% was achieved only by fast sedimentation of the granules; this performance highlighted the viability of the granular activated algae system for sustaining a microalgae harvesting procedure with neither cost nor energy inputs.