This study focuses on the stabilization of a natural hair dye derived from Lawsonia inermis L. (henna) and Indigofera suffruticosa (indigo). Although various formulations already exist, they are designed for immediate use and cannot be stored. Lawsonia, a primary component of the dye, tends to degrade after release. To ensure its stability, freeze-drying was implemented as a protective measure. Colorimetric analysis confirmed the dye’s ability to maintain an intense, uniform coloration even after multiple washing cycles. Stability tests demonstrate that freeze-drying effectively enhances the dye’s stability and capacity to retain its physical properties and color under various environmental conditions, demonstrating its potential for long-term use. The dye’s pH (5.05) aligns with the natural pH of hair, promoting cuticle sealing and improving hair health. Cytotoxicity tests confirmed the dye’s safety, showing no harmful effects. Gray hair exhibited a total color difference (ΔE) of 64.06 after the initial application, using natural gray hair as a reference. By the third application, ΔE increased to 69.86 and gradually decreased to 68.20 after 15 washing cycles, highlighting its long-term durability. Gray hair exposed to 720 h of UV radiation showed a ΔE of 17.34, whereas dyed gray hair exhibited a ΔE of 2.96 compared to non-UV-exposed samples. This indicates superior resistance to color degradation in dyed hair. Also, SEM imaging revealed the dye’s restorative effects, progressively improving hair cuticle structure with each application.