The administration of systemic antimicrobials as adjuncts to mechanical treatments of periodontitis and sites with adverse clinical results leads to improved outcomes. This study aimed to assess the antimicrobial susceptibility of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythia found in periodontitis patients to amoxicillin, metronidazole, azithromycin, and moxifloxacin. A total of 76 patients diagnosed with generalized periodontitis were included in the study. Subgingival samples were processed by culture. The epsilometric method was implemented to explore the susceptibility to amoxicillin, metronidazole, azithromycin, and moxifloxacin. A total of 141 isolates from 76 patients were evaluated: P. gingivalis (61), T. forsythia (43), and A. actinomycetemcomitans (37). The results showed a complete susceptibility of A. actinomycetemcomitans, P. gingivalis, and T. forsythia to moxifloxacin. However, the isolates presented a reduced susceptibility to the other antimicrobials investigated. A total of 70.3%, 40.5%, and 89.2% of the A. actinomycetemcomitans isolates were resistant to amoxicillin, azithromycin, and metronidazole, respectively. P. gingivalis samples showed relatively similar rates of resistance to amoxicillin (24.6%), azithromycin (21.3%), and metronidazole (24.6%). Similarly, 25.6%, 21%, and 25.6% of T. forsythia isolates were resistant to amoxicillin, azithromycin, and metronidazole, respectively. These findings show that moxifloxacin may be a promising antimicrobial against P. gingivalis, T. forsythia, and A. actinomycetemcomitans for the treatment of periodontitis. However, amoxicillin, azithromycin, and metronidazole were less effective, especially against A. actinomycetemcomitans in vitro.