Periodontal and peri-implant diseases are plaque-induced infections with a high prevalence, seriously impairing people's quality of life. The diode laser has long been recommended as adjunctive therapy in treating periodontitis. However, the optimal combination of usage mode (inside or outside periodontal pocket) and application regimen (single or multiple sessions of appointment) has not been described in detail. Meanwhile, probiotic Lactobacillus is regarded as a potential adjuvant in the management of the peri-implant disease. Nonetheless, a detailed protocol for an effective probiotic application is lacking. This article aims to summarize two clinical protocols. For periodontitis, the optimal collaboration of laser usage mode and application regimen was identified. Regarding peri-implant mucositis, a combined therapy containing professional topical use and home administration of probiotic Lactobacillus was established. This updated laser protocol clarifies the relationship between the treatment mode (inside or outside the periodontal pocket) and the number of laser appointments, further refining the existing diode laser therapy. For inside pocket irradiation, a single session of laser treatment is suggested whereas, for outside pocket irradiation, multiple sessions of laser treatment provide better effects. The improved probiotic Lactobacillus therapy resulted in the disappearance of swelling of the peri-implant mucosa, a reduced bleeding on probing (BOP), and an obvious reduction and good control of plaque and pigmentation; however, probing pocket depth (PPD) had limited improvement. The current protocol should be regarded as preliminary and could be further enhanced.