Background: Primary alveolar bone grafting inhibits craniofacial growth. However, its effect on craniofacial growth in one-stage cleft lip and palate protocols is unknown. This study investigated whether primary alveolar bone grafting performed during one-stage unilateral cleft lip and palate repair negatively affects growth up to 6–11 years old. Methods: The craniofacial growth, dental arch relationship and palatal morphology at 6–11 years old in children with unilateral cleft lip and palate were compared retrospectively. Two cohorts after a one-stage protocol without (Group A) and with (Group B) primary bone grafting at the same center were compared. Further, cephalometric measurements for growth were compared with an external cohort of a one-stage protocol and a heathy control. Results: Group A comprised 16 patients assessed at 6.8 years (SD 0.83), and Group B comprised 15 patients assessed at 9 years (SD 2.0). Cephalometric measurements indicated similar sagittal maxillary growth deficits and a significant deviation in maxillary inclination in both groups compared to the healthy group. Moderate to severe changes in palatal morphology were observed in 70% of the members in both groups. Conclusion: Omitting primary alveolar bone grafting under the one-stage protocol with two-flap palatoplasty studied did not improve growth at 6–11 years. The results implicate two-flap palatoplasty with secondary healing as having greater adverse effects on growth than primary alveolar bone grafting. Dental and palatal morphology was considerably compromised regardless of primary alveolar bone grafting.