The objective of this work was to explore the storage properties of a structured oil-in-water emulsion containing both water- and fat-soluble bioactive compounds from bilberries (Vaccinium myrtillus L.). Bilberry seed oil (BSO) was dispersed in a continuous aqueous phase of anthocyanins (AC) and whey protein isolate. The microstructure was evaluated using light microscopy and the effect of anthocyanins on lipid oxidation and microbial growth was investigated. The results showed that it was possible to generate a stable emulsion structure that resisted phase separation during 25 weeks of storage. Gas chromatography–mass spectrometry measurements of the fatty acids in the BSO during storage showed that AC had a protective effect against lipid oxidation. The AC did not have an antimicrobial effect against the investigated strains Zygosaccharomyces bailii (ATCC 42476) and Aspergillus niger (ATCC 6275 (M68)).