Encapsulation of polar and non-polar bioactive compounds from bilberries was achieved by designing microcapsules with bilberry seed oil (BSO) distributed in an aqueous phase of anthocyanins (AC) stabilized by whey protein isolate (WPI). Non-thermal emulsification method (o/w/o) was developed and the effect of pH (3 or 4.5), concentration of WPI (8.4–10.8% w/w), addition of AC (72–216 ppm) and emulsifier on the structure-forming kinetics, resulting microstructure during storage and after centrifugation and washing was investigated. Agglomeration of BSO was observed in all microcapsules at pH 4.5 due to slow gelling process and in samples at pH 3 at low concentrations of WPI (≤8.4%). Capsules with pH 3 (9.6–10.8% WPI) had weak structures but as the gelling process was faster, it generated an even distribution of BSO droplets. All samples at pH 4.5 and samples with WPI concentration ≥10.8% at pH 3 exhibited intact structures after centrifugation and washing.