This systematic review investigates the impact of non-surgical and surgical treatments on the oral microbiota and microbiome in periodontitis management. The review analyzed 5152 papers from PubMed, Scopus, and Web of Science, narrowing down to 22 articles. Key findings include that periodontitis alters the oral microbiome, increasing antibiotic resistance and promoting harmful bacteria. Treatments like scaling and root planing (SRP), especially with minocycline, improve clinical outcomes by reducing harmful bacteria. Comprehensive mechanical debridement with antibiotics, probiotics, and bone grafts enhances periodontal health. Personalized treatment strategies and microbial analysis are crucial for effective periodontal management and antibiotic resistance control. The review highlights the role of the oral microbiota in periodontitis development and progression, emphasizing the need for understanding microbial dynamics to improve treatment outcomes. Non-surgical treatments like SRP reduce pathogenic bacterial load and promote a healthier oral environment. Surgical interventions can significantly alter the microbiota, leading to more favorable and long-lasting recolonization. Probiotics, paraprobiotics, postbiotics, and ozonized materials are effective in modulating the host's immune system, encouraging tissue regeneration, and reducing harmful bacteria. Studies show that periodontal therapy significantly reduces disease-associated bacteria and shifts the microbial profile toward a healthier state. The use of probiotics and other adjunctive therapies can enhance clinical outcomes and reduce the need for invasive procedures. However, the long-term effects of these treatments on the oral microbiota require further research. The review underscores the importance of personalized treatment strategies based on microbial profiles to improve periodontal health and prevent recurrence. Overall, understanding the microbiological effects of treatments is essential for developing more effective and individualized periodontal care.This systematic review investigates the impact of non-surgical and surgical treatments on the oral microbiota and microbiome in periodontitis management. The review analyzed 5152 papers from PubMed, Scopus, and Web of Science, narrowing down to 22 articles. Key findings include that periodontitis alters the oral microbiome, increasing antibiotic resistance and promoting harmful bacteria. Treatments like scaling and root planing (SRP), especially with minocycline, improve clinical outcomes by reducing harmful bacteria. Comprehensive mechanical debridement with antibiotics, probiotics, and bone grafts enhances periodontal health. Personalized treatment strategies and microbial analysis are crucial for effective periodontal management and antibiotic resistance control. The review highlights the role of the oral microbiota in periodontitis development and progression, emphasizing the need for understanding microbial dynamics to improve treatment outcomes. Non-surgical treatments like SRP reduce pathogenic bacterial load and promote a healthier oral environment. Surgical interventions can significantly alter the microbiota, leading to more favorable and long-lasting recolonization. Probiotics, paraprobiotics, postbiotics, and ozonized materials are effective in modulating the host's immune system, encouraging tissue regeneration, and reducing harmful bacteria. Studies show that periodontal therapy significantly reduces disease-associated bacteria and shifts the microbial profile toward a healthier state. The use of probiotics and other adjunctive therapies can enhance clinical outcomes and reduce the need for invasive procedures. However, the long-term effects of these treatments on the oral microbiota require further research. The review underscores the importance of personalized treatment strategies based on microbial profiles to improve periodontal health and prevent recurrence. Overall, understanding the microbiological effects of treatments is essential for developing more effective and individualized periodontal care.