It is well known that wastewaters from the food industry are a potential source of valuable compounds, such that these wastewaters may be considered by-products awaiting the development of appropriate treatment methodologies. Whey is one of the most important polluting effluents from the milk industry because of its very high biological oxygen demand (BOD). Nevertheless, whey is rich in by-products such as whey proteins and lactose, both of which are widely used industrially. Integrated processes could permit the selective recovery of these by-products in conjunction with the generation of clean, reusable water, thus reducing the environmental impact of this wastewater. Ultrafiltration is a crucial step in the separation and recovery of whey protein and lactose, but this technology suffers from fouling problems that can reduce its performance. New technologies assisted by smart modeling and control systems could improve this ultrafiltration step. In this work, a novel system that allows the recovery of the whey protein in milk industry effluent and the disposal of wastewater was developed and tested. This system utilizes an ultrafiltration process, as this permits the purification of the effluent at room temperature, ensuring the preservation of the recovered proteins. A specially designed autoadaptive fuzzy logic controller evaluates the level of filter membrane fouling and controls a mechanical device that induces filter regeneration. Experimental testing showed that this approach permits process intensification.