Aim: To report a case series with three clinical protocols to treat combined endodontic- periodontal lesions (EPLs). Materials and methods: EPLs were treated by the same endodontic protocol and allocated in three periodontal treatment groups: Scaling Root Planning (SRP, n=15), SRP associated with Amoxicillin and Metronidazole (SRP+AMX+MET, n=16), and Open Flap Debridement (OFD, n=13). Probing pocket depth (PPD), clinical attachment level (CAL), bleeding on probing (BOP-%), plaque index (PI-%), tooth mobility (TM), and volumetric analysis of EPL by cone-beam computed tomography (CBCT) were evaluated at 30 days, 3 months, and 6 months after periodontal therapies. Results: All therapies had a significant improvement in clinical parameters showing a reduction in PPD, CAL, BOP. There was no intra- or intergroup difference in PI (p>0.05). The SRP+AMX+MET therapy showed the best results in terms of PPD reduction (p<0.05) at 6 months with a reduction in TM at 30 days, 3, and 6 months (p<0.05). Both the SRP+AMX+MET and OFD therapies promoted reduction in lesion volume (p<0.05). Conclusion: All protocols were effective in the treatment of endo-periodontal lesions. However, the endodontic treatment protocol associated with the SRP+AMX+MET therapy seems to have the best clinical and tomographic results.