Background: Extracts of medicinal plant like lemongrass offer a new choice for optional antimicrobial therapy against various oral microorganisms. The objective of this study was to assess, verify, and compare the antimicrobial effectiveness of locally administered 2% lemongrass gel and 10% doxycycline hyclate gel as an adjunct to scaling and root planing (SRP) in treating chronic periodontitis. Method: This is a double-blind parallel arm randomized controlled study. Forty subjects were randomly divided into Group A and B for 2% lemongrass gel and 10% doxycycline hyclate gel, respectively. The clinical assessments of Gingival Index (GI), Plaque Index (PI), Probing Pocket Depth (PPD), and Clinical Attachment Level (CAL) together with microbial colony counts for Porphyromonas gingivalis, Actinomyces naeslundii, and Prevotella intermedia were done at baseline, 1st month, and 3rd month follow-ups. Results: The results showed there was a significant reduction in the mean scores of GI, PPD, and CAL clinical indices from baseline to the 1st and 3rd month follow-ups in both the 2% lemongrass gel and 10% doxycycline gel groups (p < 0.05). Similarly, there was significant reduction in mean CFU scores for all periodontal pathogens from baseline to 1st and 3rd month follow-ups in both the 2% lemongrass gel and 10% doxycycline gel groups (p < 0.05). Conclusions: It could be concluded that the local delivery of 2% lemongrass gel as an adjunct to scaling and root planing is effective and comparable to 10% doxycycline gel in the treatment of chronic periodontitis.