Background: The aim of this study was to evaluate the clinical and radiological efficacy of minimally invasive surgical techniques for infraosseous defects by evaluating the effects of Emdogain (EMD) applied alone or with a xenograft, with a follow-up period of one year. Methods: Forty patients with a combined total of forty-eight intraosseous defects participated in the research. Of these, 20 participants were treated with EMD (group 1), and 28 were treated with EMD and a xenograft (group 2). The clinical measurements probing depth (PD), recession (REC), and clinical attachment level (CAL) were assessed at six sites on the tooth. Additionally, the following intraoperative clinical measurements were taken: (1) distance from the cementoenamel junction (CEJ) to the bottom of the defect (CEJ-BD) and (2) distance from the CEJ to the most coronal extension of the interproximal bone crest (CEJ-BC). The infraosseous component of the defect was defined as INTRA = (CEJ-BD) − (CEJ-BC). Results: In comparison with the baseline, both treatment options showed statistically significant improvements in reducing PD and increasing CAL. The reduction in PD was 3.25 ± 0.786 mm for group 1 and 3.29 ± 1.013 mm for group 2. In terms of CAL gain, group 1 recorded a value of 4.65 ± 1.387 mm, compared with 5.07 ± 1.631 mm in group 2. Both groups showed a noticeable increase in radiographic bone filler, with an average of 69.85 ± 17.773%. Conclusions: The two regeneration techniques were both effective for the treatment of deep intraosseous defects, encouraging more substantial filling compared with preoperative levels.