Background and Objectives. Antibiotic regimen optimization is a major concern in post extraction sequelae management following third molar surgery, mostly owing to the absence of universal guidelines. Hence, this study aimed to determine the effect of antibiotic prophylaxis using three different doses of clindamycin on the prevention of infection and other complications following mandibular third molar disimpaction. The secondary outcome was testing whether clindamycin exhibits activity in acute or chronic models of pain using the visual analog scale of pain and the necessity for post-operative rescue analgesia. The tertiary outcome was to assess clindamycin penetration into the saliva by measuring its concentration using liquid chromatography/electrospray ionization tandem mass spectrometry. Materials and Methods. A randomized, two-center, triple-blind, controlled clinical trial was conducted, in which the patients were randomly allocated to three groups: I, receiving 150 mg clindamycin every 8 h; II, receiving 300 mg clindamycin every 8 h; and III, receiving 600 mg clindamycin every 12 h. Each group continued the therapy for five days. Results. An overall decrease in the risk of infection and other post-operative complications, such as trismus, edema, dysphagia, and lymphadenopathy, was achieved, with the best results in group I. Conclusion. As no statistical association was observed between clindamycin concentration in saliva and degree of post-operative inflammation, clindamycin concentration, or pain intensity, smaller doses of clindamycin administered over shorter time periods is recommended.