Objective: This is the first study to systematically evaluate the timing of secondary alveolar bone grafting (SABG) based on canine root mineralization stages (R-value), assessing its impact on bone graft preservation, canine eruption, and space closure in patients with cleft lip and palate (CLP). Materials and methods: This retrospective single-center cohort study included 104 patients with unilateral or bilateral CLP (127 cleft sites). Orthopantomograms and clinical records were evaluated at three stages: pre-SABG, six months post-SABG, and post-orthodontic treatment. The R-value was classified as R = 0,25 − 1,0, corresponding to 25–100% root development, respectively. Assessed parameters included the canine mineralization stage, axis-angulation and vitality, limbus height, probing depths, and space closure strategy. Group comparisons were performed using t-tests. Results: Early SABG (R ≤ 0,5) yielded significantly higher orthodontic space closure rates (71% versus 25% with late SABG, p < 0,05) with better graft preservation, but was associated with increased canine impaction (18,6% in lateral incisor agenesis cases). The mean axis-angle of cleft-side canines differed significantly between orthodontic and prosthodontic space closure (81,3° vs. 91,0°, t = 5,702). Limbus alveolaris height was reduced when SABG occurred after root completion (R = 1,0, t = 4,234). Periodontal probing depths remained < 3 mm, and canine vitality was preserved in all groups. Conclusions: Early SABG, timed according to canine mineralization, supports alveolar bone preservation and space closure without compromising periodontal health. Clinical relevance: Tailoring SABG timing based on dental development can optimize orthodontic and prosthodontic outcomes in patients with CLP.