Marginal and periapical periodontal diseases cause massive destruction of tooth tissues and surrounding tissues, such as alveolar bone and maxillary sinus floor, visible on radiographs. Lesions involving the apical and marginal periodontium are endo−perio (EPL) lesions. This study aimed to compare the treatment efficacy of endo−perio lesions using a standard treatment protocol and a standard diode laser-assisted treatment protocol. The 12 patients were divided into the study (a) and control (b) group. Periodontal indices, tooth vitality and mobility, occlusal status, and radiographic diagnosis were evaluated. Standard EPL treatment was then performed—without (a) and with (b) the use of diode laser (940 nm). Again, after six months, the above-mentioned parameters were evaluated and compared. The treatment of endo−perio lesions is a significant challenge for modern dentistry. Diode lasers are increasingly used in addition to traditional treatment methods. The conventional use of a 940 nm diode laser with an average power of 0.8 W in pulsed mode allows for the depth of periodontal pockets to be reduced. In addition, the use of a diode laser has a significant effect on tooth mobility and reduces bone loss.