IntroductionThe current gold standard treatment for patients with orofacial clefts is surgical repair of the palatal defect (uranostaphylorrhaphy), which is associated with growth defects and hypoplasia of the maxillofacial structures. This trial aims to evaluate the potential of a bioengineered artificial palate mucosa, created through tissue engineering with autologous stromal and epithelial cells and nanostructured fibrin–agarose biomaterials, to enhance treatment outcomes for patients with unilateral cleft lip and palate.Methods and analysisThis phase I-IIa clinical trial aims to evaluate the feasibility and biosafety of a procedure involving grafting bioartificial palate mucosa onto the areas of denudated bone in patients undergoing uranostaphylorrhaphy. The control patients will undergo standard surgical treatment. Five patients will be included in the first biosafety phase. In the second phase, 10 patients will be randomly assigned to the intervention or control group (1:1). The intervention group will undergo standard surgical treatment followed by the application of autologous bioartificial palate mucosa. Feasibility will be analysed at the time of surgery. Nine postimplant visits will be scheduled over a 2-year follow-up period, in which local and systemic biosafety will be investigated by determining graft evolution, including signs of necrosis, rejection, inflammation and patient factors. Preliminary signs of efficiency will be explored by sequentially evaluating craniomaxillofacial development, hearing impairment, speech capability and quality of life of the family. The research will be published in journals and posted in the relevant repositories when available.Ethics and disseminationThis study has been approved by the Committee of Ethics in Research with Medicinal Products (CEIm) and authorised by the Spanish Medicines Agency (AEMPS). The results of this study will be published in peer-reviewed journals.Trial registration numberNCT06408337; ClinicalTrials.gov: EuclinicalTrials. eu: 2023-506913-23-00.