Understanding the bioactive partitioning between the phases of an emulsion system underpins strategies for improving the efficiency of bioactive protection against degradation. We analysed partitioning of β-carotene in emulsions with various formulations in-situ using confocal Raman microscopy (CRM). The partitioning of β-carotene into the aqueous phase of emulsions increased when whey protein isolate (WPI) was heat or high pressure-treated prior to emulsion formation. However, increasing the concentration of high pressure-treated WPI reduced the β-carotene partitioning into the aqueous phase. Increasing the solid fat content in the carrier oil favoured the migration of β-carotene into the aqueous phase. The use of WPI as the emulsifier resulted in a greater partitioning of β-carotene into the aqueous phase compared to when Tween 40 was the emulsifier. This study demonstrates that partitioning of β-carotene between the aqueous and oil phase is dependent on the characteristics of the oil phase, emulsifier type and processing.