The aim of this two-arm parallel trial was to evaluate enamel demineralization in fixed orthodontic treatment using an indirect bonding technique in comparison to a direct bonding technique by the quantitative light-induced fluorescence (QLF) method. Fifty-six patients who needed fixed orthodontic treatment were randomly separated into either the direct bonding group or the indirect bonding group. The presence and extent of lesions on the buccal surfaces of all teeth, except the molar teeth, were assessed. The percentage of fluorescence loss (ΔF and ΔFmax), the degree of demineralization (ΔQ) and lesion area (WS area) were determined using the system's software. The data were analysed with the Wilcoxon signed-rank and Mann-Whitney U-tests (P < 0.05). Treatment with a direct bonding or an indirect bonding technique. This study was completed with 25 patients in the indirect bonding group (12 females, 13 males; mean age: 15.42 ± 1.71 years) and 26 patients in the direct bonding group (12 females, 14 males; mean age: 14.73 ± 1.65 years). In the indirect bonding technique, a few teeth (especially mandibular left canine: 50.45 ± 93.48; 95% confidence interval: -12.35 and 113.26) were found to develop significant white spot lesion (WSL) formation (P < 0.05). However, the number of teeth with demineralization was higher in the direct bonding group (P < 0.05). The bonding procedures used in the indirect bonding technique contribute to reducing the degree of WSL formation. Further, the use of flowable composite adhesives in this bonding process is more effective at reducing the appearance of WSLs than in cases where conventional composite adhesives are used. The limitation of our trial may be the small sample size and the short follow-up time for the patients. No harms were detected during the study. The protocol was not published before trial commencement. This trial was registered post hoc at 'Clinical Trials' (http://www.clinicaltrials.gov), registration number (ID): NCT03738839.