This study was conducted to examine floc-harvesting performance by three separation technologies, namely sedimentation, centrifugation, and membrane filtration, for biofloc generated from a BFT system in aquaculture. According to the experimental results, sedimentation demonstrated the poorest harvesting performance with the lowest energy consumption; centrifugation showed the highest harvesting performance with the highest energy burden; membrane filtration achieved better harvesting performance than sedimentation and better energy efficiency than centrifugation. In terms of large-scale floc recovery, a two-step harvesting process utilizing centrifugation with membrane filtration was found to be a reliable way to overcome the limitation of sedimentation and obtain moderate energy-efficiency. Overall, the energy-consuming aspects of the floc-recovery process on an industrial scale should be concerned, even though the use of biofloc as an aquaculture feed would be a positive in terms of an environment-friendly approach to recycling of aquaculture wastewater.