Background: This study evaluated the color stability and nanoleakage of a self-adhering bioactive flowable composite (Beautifil Kids SA), a bioactive flowable composite (Beautifil Flow), and a conventional flowable composite (3M Filtek Supreme Flowable Restorative) used for Class V restorations in primary molars. Methods: Seventy-two extracted primary molars with standardized buccal Class V cavities (2 × 2 mm) were randomly divided into three groups (n = 24). Color stability was assessed by spectrophotometry using the CIELAB system after pH cycling and 1,000 thermocycles. Nanoleakage was assessed by scanning electron microscopy (SEM) and ImageJ analysis after silver nitrate penetration and thermocycling. Results: For color stability, the self-adhering bioactive flowable composite showed the highest ΔE (4.48 ± 0.26), followed by the bioactive flowable composite (3.57 ± 0.20) and the conventional flowable composite (3.08 ± 0.20). For nanoleakage, the highest mean value was recorded for the bioactive flowable composite (103.0 ± 8.58), followed by the conventional flowable composite (94.29 ± 11.27), whereas the self-adhering bioactive flowable composite showed the lowest value (87.86 ± 9.23). Conclusion: Within the limitations of this in vitro study, Beautifil Kids SA showed the highest color change but the lowest nanoleakage value among the tested materials, indicating a trade-off between color stability and interfacial sealability.