Different beetroot derivatives have been used in yogurt, improved the nutritional-related properties, and challenged the functionality as well as acceptability. However, fresh water-soluble-fraction in beetroot (WFB) in yogurt has never been reported. The study evaluated the functionality and acceptability of yogurt enriched with WFB at different concentrations (10, 20, and 30 g/L), which were evaluated at 5 °C for 0, 6, 12, and 18 days of storage. Compared to control, the addition of WFB significantly decreased the pH from 4.1–4.9 to 2.3–4.2 and increased total acid content from 2.1%–2.5% to 3.0%–3.6%, total lactic acid bacteria (LAB) count from 6.6–6.9 to 6.8–7.1 (lg(CFU/mL)), vitamin C content from 2.3–3.1 to 2.4–4.1 mg/100 g, DPPH radical scavenging activity from 23.5%–50.0 % to 61%–69%, and hedonic acceptability. Total LAB count rose from 6.6 (lg(CFU/mL)) to reach the highest at 30 g/L addition which ranged of 6.8–7.1 (lg(CFU/mL)). 20 g/L of WFB generated a more stable vitamin C during the 18 days of storage period. During the 18 days of storage, the 20 and 30 g/L of WFB yogurt had a higher stability of antioxidants. In conclusion, 20 and 30 g/L of WFB can be expected to enhance the stability of nutritional-related properties of the yogurt with a higher acceptability. Low amount of WFB contributed to an attractive performance from consumer perspective.