Studies investigating the application of blue pea flower anthocyanins in fermented dairy products are limited. In this study, the application of anthocyanin extracts from blue pea flower (Clitoria ternatea) in yoghurt and fermented milk at 1 and 2% (w/v) concentrations was investigated and compared to a commercial blue colourant from spirulina. The total anthocyanin content (TAC), antioxidant activity (DPPH free radical and ferric reducing antioxidant power assays), pH, titratable acidity, syneresis, colour, and viable cell count were measured at 6 days intervals for 30 days at 4 °C storage. The TAC of yoghurt with blue pea flower anthocyanin extract demonstrated high stability, but the TAC of fermented milk with blue pea flower anthocyanin extract decreased significantly. The yoghurt and fermented milk with blue pea flower anthocyanin extract demonstrated higher antioxidant activity than the negative control and samples containing spirulina. The total colour change (ΔE) of yoghurt with blue pea flower anthocyanin extract was less than that of yoghurt containing spirulina during storage. However, the colour of fermented milk with blue pea flower anthocyanin extract was less stable than samples containing spirulina. The average colour acceptability of yoghurt and fermented milk containing 2% (w/v) blue pea flower anthocyanin extracts and those containing spirulina colourant was not significantly different. Therefore, an anthocyanin extract from blue pea flowers at 2% (w/v) concentration was a better blue colourant than spirulina in yoghurt. Spirulina was a better colourant compared to blue pea flower anthocyanins for fermented milk.