Recovery followed by re-use of process-water obtained from dairy effluents by means of reverse osmosis technology is one route that can provide the dairy industry with the possibility to reach sustainable water regimes. However, membrane fouling is a phenomenon that limits both the efficiency and increases the running costs of such reverse osmosis units and can potentially alter the quality characteristics of permeate water. In this paper, several industrial-scale RO membranes used for recovery of process-water from whey UF permeate have been examined for their fouling tendency. At the end of a complete clean-in-place (CIP) protocol based on alkaline-acid formulations, biofouling appears to be the main issue in the investigated RO-elements. Between 4.19 and 5.69 log₁₀ (CFU cm⁻²) of viable microorganisms still remained on the membrane retentate surface and, more surprisingly, evidence of significant contamination was found on permeate side of these particular membranes. Microbiological analysis indicate that minor loads of microorganisms do pass into the permeate streams but final UV treatments ensured final process-water with non-detectable levels. There is a need for optimization of cleaning procedures and finding the best compromise for achieving surface disinfection while still preserving membrane integrity and not compromising the water quality.