Introduction Humankind is suffering from the misuse and overuse of antibiotics, leading to antibiotic resistance. At this point, probiotics, if found effective, can lead to a better future. Probiotics are nothing but a colony of living-friendly bacteria. Lactobacillus reuteri is essential for use as a probiotic among many healthy bacteria. This study aims to compare the effectiveness of probiotics in periodontal treatment. Methods One hundred smokers diagnosed with chronic generalized periodontitis were randomly assigned into two groups. Group A received a seven-day course of amoxicillin 500 mg three a day and metronidazole 500 mg twice daily, followed by 30 days of probiotics, while Group B received a placebo antibiotic for seven days and 30 days of L. reuteri probiotics (2×10⁸ CFU daily). Periodontal parameters, including plaque index (PI), gingival index (GI), probing depth (PD), attachment loss (AL), and bleeding on probing (BOP), were utilized to asses at baseline, month one, and month one. Baseline differences were adjusted using the generalized estimating equation (GEE) model. Results At month three, Group B (probiotics) showed a significantly lower PI (0.52±0.49 vs. 0.88±0.52, p<0.001) and a 23% greater reduction in PD (p=0.004) compared to Group A (antibiotics + probiotics). These findings highlight the effectiveness of probiotics alone in improving periodontal health in smokers. Conclusions Both groups showed equal effectiveness in improving periodontal health. Hence, probiotics should be preferred over antibiotics.