Objective: The current study aimed to evaluate the effects of methanolic extracts of Cinnamon and Cloves mixed with Fluoride Varnish Containing CPP-ACP (MI Varnish™) treatments on the enamel microhardness and color. Material and Methods: Forty enamel specimens obtained from twenty human impacted third molars were randomly divided into four groups (n = 10) according to surface treatment: (G1) MI Varnish™ mixed with methanolic extract of Cinnamon; (G2) MI Varnish™ mixed with methanolic extract of Cloves; (G3) MI Varnish™ mixed with methanolic extracts of Cinnamon and Cloves meanwhile (G4) MI Varnish™ alone. Specimens were subjected to pH cycling. Color (ΔE) and surface microhardness were measured for each specimen at base line, after demineralization and post treatment. Results: The highest microhardness values presented in MI Varnish alone (G4) and MI Varnish™ mixed with methanolic extracts of Cinnamon and Cloves (G3) without any significant difference between them, followed by MI Varnish™ mixed with methanolic extract of Cinnamon (G1), while the lowest hardness values were found in MI Varnish™ mixed with methanolic extract of Cloves (G2). There was an increase in ΔE3 values for all groups. Conclusions: Under the limitations of the current study, application of Cinnamon and Clove as herbal antibacterial medicaments does not affect enamel microhardness negatively when added with the MI paste at certain ratio. Meanwhile, unacceptable color changes of enamel surface are expected.