Aim: To assess the efficacy of omega-3 (ω-3) polyunsaturated fatty acid (PUFA) as a dietary supplement vs local drug delivery (LDD) agent based on periodontal and microbiological parameters in patient with generalized chronic periodontitis. Materials and methods: Around 10 systemically healthy individuals diagnosed with “generalized chronic periodontitis” were selected, and after randomization, five patients were allotted to each group. Group I (n = 5) patients were given ω-3 PUFA capsules as a dietary supplement of 500 mg BD orally after scaling and root planing (SRP), and in group II (n = 5), ω-3 PUFA oil was placed as LDD after SRP. Pocket depth, clinical attachment level (CAL), gingival, and plaque index (PI) were recorded, and colony-forming unit (CFU) of Porphyromonas gingivalis were recorded at baseline, after 3, 4, and 6 weeks from plaque samples. Data were recorded and statistically analyzed. Results: Both groups showed a reduction in bleeding index, pocket depth, PI, CAL, and P. gingivalis CFU count at 3, 4, and 6 weeks follow-up, with more reduction in group II. Further statistically significant reduction was seen at a 6-week follow-up in group II in PI with a p-value of 0.023 and P. gingivalis CFU counts with a p-value of 0.024. Conclusion: It may be concluded that ω-3 PUFA is more efficacious as an LDD agent compared to a dietary supplement and showed a significant reduction in periodontal and microbiological parameters. Clinical significance: Till now, ω-3 fatty acid was used as a dietary supplement with a dose of 500 mg BD for 1–2 months. Further, in the present study, it has been used as an LDD agent in periodontitis. The potential of ω-3 fatty acid, due to its host modulation factors, has increased in management as an adjunct in the treatment of periodontitis.