There has been a growing interest in casein fractions (α_S-, β- and κ-casein) due to their various techno- and bio-functional properties and as source for bio-active peptides. Several methods for isolating and purifying caseins have been reported. However, there is still room for improvement regarding purity and yield. In this study, three casein fractions were obtained by selective precipitation. A continuous process generating three major casein fractions using a temperature-controlled decanter centrifuge for separation was developed and suitability of the experimental setup was established. The process stability evaluated and the effect of operational parameters of the decanter on the separation process was investigated. The enrichment of the fractions was optimised by adjusting the operational parameters, e.g., inner weir diameter, centrifugal force and differential speed. The purity and yield of the fractions obtained were 39.6% and 96.1% for α_S-casein, 92.1% and 27.5% for β-casein and 39.2% and 54.1% for κ-casein, respectively.