The use of autogenous grafts from the palate for the reconstruction of gingival tissues is considered the gold standard for various periodontal and peri-implant reconstructions. Given the current aging of the population, it is essential to understand the cellular mechanisms responsible for the repair response in oral tissues and how they are affected by systemic diseases, such as diabetes mellitus (DM). The objectives of the present study, conducted through a controlled clinical trial, are to characterize and compare the closure of open wounds in the palatal mucosa of diabetic and non-diabetic patients. This will be achieved through clinical analyses, patient-centered parameters, inflammatory biomarkers, and wound microbiome composition. To accomplish this, 50 patients will be divided into two groups: the Diabetic Group (D; n = 25), where diabetic patients will undergo surgery for mucogingival defect correction with the addition of a free gingival graft, and the Control Group (GC; n = 25), where normoglycemic patients will undergo surgery for mucogingival defect correction with the addition of a free gingival graft. The groups will be compared regarding clinical parameters, patient-centered measures, including remaining wound area, epithelialization, tissue thickness, immature wound area, tissue edema, early wound healing index, postoperative discomfort, quality of life, number of analgesics, and sensitivity of the operated area over a 3-month period. Furthermore, the wound biofilm will be described through microbiome analysis, and tissue, saliva, and wound exudate biomarkers will be characterized. Descriptive statistics will be expressed as mean ± standard deviation, clinical evaluations will be performed using repeated measures ANOVA, and patient-centered parameters will be assessed using the T-test. Finally, multiple linear regression and correlation tests will be employed.