(1) Background: The prevention of demineralizing lesions at the enamel structure level continues to represent a challenge in daily dental practice. When bacteria influence the pH level, this will decrease below the threshold for remineralization and the dissociation of hydroxyapatite will occur with a high percentage of phosphate and calcium loss. These elements continue to be studied by many authors in order to obtain a working protocol that will lead to their stabilization at the level of the enamel structure, thus preventing the demineralization process. The aim of this study is to evaluate and compare the influence of two types of laser wavelengths on the surface morphology and mineral components of the enamel through an examination with scanning electron microscopy (SEM) and energy-dispersive X-ray spectrometry (EDX). (2) Methods: Thirty permanent human incisors extracted for periodontal reasons from patients aged 25–40 years old were selected for this study. Metallic brackets (SS Standard 022 Slot, OC Orthodontics, McMinnville, OR, 97128, USA) were bonded onto each tooth. The buccal surface was randomly assigned three sections: Section A—negative control (no treatment), section B—treated with 980 nm Gallium–Aluminum–Arsenide diode laser (a 300 µm optic fiber was used with 0.8 W output power, energy density of 5.33 J/mm2, in continuous mode, for 30 s, oriented perpendicularly to the enamel surface in contact mode) (KaVo GENTLEray 980 Diode Laser, Kaltenbach & Voigt GmbH, Biberach, Germany), and section C—treated with Nd:YAG laser (a 300 µm fiber was carried out at a 1 mm distance from the enamel surface with 0.75 W power, 75 mJ pulse energy, pulse repetition rate of 10 Hz, 5 J/mm2 fluency, average exposure time of 30 s, and water cooling assisted) (LIGHTWALKER AT S, M021-5AF/1 S, Fotona d.o.o, Ljubljana, Slovenia). The elements evaluated in this study were calcium (Ca), phosphate (P), oxygen (O), and carbon (C). A one-way analysis of variance, paired t-tests, and independent t-tests were carried out to evaluate the results using the SPSS 19 IBM Statistical package software for Microsoft. (3) Results: The evaluation of the data indicated that both wavelengths produced an increase in Ca wt% (for diode laser the mean of Ca wt% before irradiation was 21.06, while that after treatment reached 28.24; and for Nd:YAG laser, the mean of Ca wt% before irradiation was 21.31, while that after treatment reached 33.88); as well, the 980 nm diode laser decreased P wt% (from 17.20 before irradiation to 16.92 after irradiation) and the Nd:YAG laser increased P wt% (from 17.46 before irradiation to 18.28 after irradiation). These results showed a statistically significant difference at the p < 0.05 level. (4) Conclusions: It can be concluded that the best improvement of enamel chemical composition was obtained with Nd:YAG irradiation.