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BACKGROUND Although nonfat milk has been utilized worldwide in the industrial dairy process, little is known about the effects of fat separation on skim milk's structural and digestive properties during further manufacturing process. This study investigated the effects of the manufacturing process on the structure and in vitro digestion properties of skim goat milk, particularly emphasizing on fat separation. RESULTS It was found that changes in surface charge and hydrophobicity of milk proteins caused by fat separation resulted in oxidation and aggregation in the subsequent homogenization, heat and spray drying processing, which further affected its digestibility. Compared with the separation by dish separator (DS), skim milk after tubular centrifugal separation (CS) showed a higher initial and final digestibility. Furthermore, CS samples had a lower surface hydrophobicity level and higher free sulfhydryl content, ζ-potential, and average particle size (P < 0.05). Goat milk protein after CS was more readily oxidized and aggregated during the subsequent homogenization, heat treatment, as evidenced by the higher carbonyl content and particle size. Additionally, CS converted more β-sheets to α-helices, thus promoting the aggregation of oxidized skim milk protein. CONCLUSION The the skim milk after CS and DS demonstrated different structural and digestive properties. Skim goat milk products after CS were more susceptible to oxidant-induced protein structural changes, resulting in higher protein digestibility. These findings provided insights into the mechanism involved in the control of gastric digestion of skim milk during manufacturing process instead of additives addition. This article is protected by copyright. All rights reserved.