This study aimed to evaluate the effect of self-assembling peptide P11-4 (SAP) in the therapy of initial smooth surface caries (white spot lesions, WSL) following orthodontic multibracket treatment. Twenty-three patients (13f/10m; average age 15.4 years) with at least two teeth with WSL were recruited for the randomised controlled clinical trial with split-mouth design. In opposite to the control teeth, the test teeth were treated with SAP on Day 0. The primary endpoint was the impedance measurement of WSL using customised tray to ensure reproducibility of the measurement location. The secondary endpoint was the morphometric measurement of WSL using a semi-automated approach to determine the WSL size in mm2. Treatment effects were adjusted for site-specific baseline values using mixed models adapted from the cross-over design. Test WSL showed a mean baseline impedance value of 46.7, which decreased to 21.1, 18.4, and 19.7 after 45, 90, and 180 days, respectively. Control WSL showed a mean baseline value of 42.0, which decreased to 35.0, 29.5, and 33.7, respectively. The overall treatment contrast was -13.7 (95% CI: -19.6 - -7.7; p < 0.001). For the secondary endpoint, the test WSL size decreased from 8.8 at baseline to 6.5 after 180 days. The control WSL decreased from 6.8 to 5.7, respectively. The related treatment contrast was -1.0 in favour of test WSL (95% CI: -1.6 - -0.5; p = 0.004). The treatment of initial carious lesions with self-assembling peptide P11-4 leads to superior remineralisation of the subsurface lesions compared with the control teeth.