The aim was to investigate the ability of self-assembling Peptide P11-4 Matrix (SAPM) to remineralize artificial initial caries lesions compared to the use of fluoride varnish. Volunteers were recruited for this randomised, cross-over in situ trial. Bovine specimens, half including orthodontic brackets, were recessed on the buccal aspects of mandibular appliances. Specimens included internal sound enamel control, a demineralised control and a part exposed during the in situ phase. Each phase lasted four weeks, followed by a one-week washout. Treatment groups were: A: negative control, no treatment,B: positive control, 22,600 ppm fluoride varnish,C: test group, 1,000 ppm SAPM. Laser fluorescence values (LF) were measured before/after demineralisation, and after the in situ period. Micro-CT analysis was used to assess mineral changes within the specimens after the in situ phase. In specimens without brackets, ΔLF values after in situ phase were: A: +5.28, B: +0.85, C: -2.89. Corresponding ΔLF for specimens with brackets were: A: +5.77, B: +1.30, C: -3.15. LF-values between groups significantly differed from each other (p < 0.0001) after the in situ phase. Micro-CT analysis yielded no significant difference among groups for specimens without brackets. For specimens with brackets, the test group showed significantly more remineralisation than the negative (p = 0.01) and positive control (p = 0.003). Within the limitations of the study, SAPM showed prevention of caries and remineralisation of enamel around orthodontic brackets.