White-spot-lesions (WSL) are a common complication associated with orthodontic treatment. In the current study, the remineralization efficacy of a BiominF® paste was compared to the efficacy of a fluoride gel. Methods: Orthodontic brackets were bonded to 60 human premolars buccal surfaces, which were covered with varnish, except a small treatment area (3 mm2). All specimens were challenged by a demineralization solution for 4 days. Specimens were assigned into 4 groups: BiominF® paste, Fluoride (4-min application), fluoride (twenty four hours application), and the control (n = 15). After cross-sectioning, enamel slabs having a thickness of approximately 100–120 μm were obtained. A TMR (Transverse Micro Radiography) technique was used to observe the sub-surface enamel lesions’ depth and mineral density, and their response to the remineralization protocols. One way ANOVA was used to analyze the results (α = 0.05). The top and the cross-sectional surfaces were observed using SEM/EDS. Results: Specimens treated with BiominF® paste showed significant decrease in delta z values, however lesion depth showed no significant difference when compared to the other three groups (p < 0.05). SEM/EDS observation showed the formation of crystal like structures on top of enamel demineralized surfaces, when treated with BiominF® paste. In conclusion BiominF® paste can be considered an effective remineralizing agent for white spot Lesions.