The introduction of membrane filtration during infant milk formula (IMF) processing represents an innovative approach to increasing native protein content compared to standard IMF. The objective of this study was to compare IMF powder produced using a standard process and IMF produced from raw bovine skim milk with added whey protein isolate using a split-stream process incorporating a ceramic 1.4 μm filter followed by a polyvinylidene difluoride polymeric 0.2 μm filter. Retentates from 0.2 μm microfiltration (MF) were blended with fat, lactose, and minerals and subsequently high-temperature treated (125 °C × 5 s). The heat-treated retentate was merged with the permeate from the 0.2 μm MF, homogenised, and spray-dried (referred to as membrane-filtered IMF or MEM-IMF). A control IMF was also produced using standard treatment (referred to as high-temperature IMF or HT-IMF) without membrane filtration. Both IMF products were characterised by high-performance liquid chromatography, particle size, and enzyme activity assays. MEM-IMF powder had significantly higher amounts of native (1.1 g per 100 g powder) and monomeric (1.48 g per 100 g powder) whey proteins when compared to 0.18 and 0.46 g per 100 g powder in HT-IMF, respectively. MEM-IMF also exhibited a lower degree of protein aggregation compared to HT-IMF. Comparison of microbial and Maillard by-products markers demonstrated that a safe IMF product could be produced at scale, although levels of the Maillard by-product marker, carboxymethyl-lysine, were not significantly reduced in MEM-IMF. This study demonstrates how membrane filtration can be used to retain native proteins during IMF manufacture.