Background: Over the past two decades, with the collaboration between periodontists and orthodontists, the concept of a surgically facilitated orthodontic therapy (SFOT) approach was developed, which not only provides acceleration in tooth movement as a result of a stimulated regional acceleratory phenomenon but also increases the alveolar bone volume for orthodontic tooth movement range by bone grafting. Despite the benefits, hard and soft tissue defects can sometimes be observed in patients post SFOT, especially among groups with thin periodontal phenotypes. Methods: In the current study, we compared the traditional SFOT with allograft only and the modified SFOT with allograft and collagen matrix to explore if the addition of a collagen matrix between the bone graft and periodontal flap could achieve soft tissue augmentation and reduce the prevalence of the complications of SFOT. Six patients were initially enrolled in the current study. Four patients showed up for the 1-week and 2-week post-operation evaluations. However, only one subject of each group agreed on periodontal evaluation by bone sounding and CBCT during the 6-month follow-up appointment. Results: Six months post SFOT, the patient with the modified SFOT presented with a larger amount of soft tissue thickening compared to the patient with traditional SFOT. However, the location of bone generation was different between groups, with the modified SFOT group presenting with bone generation more apically. In addition, patients with modified SFOT reported a more severe level of discomfort than patients with traditional SFOT. Conclusions: The modified SFOT may potentially improve soft tissue phenotype; however, further modifications are needed to reduce the patient’s discomfort level and to ensure that bone particles are contained more incisally.