A controlled-release device (CRD) containing chlorhexidine gluconate, such as PerioCol(™)CG (Eucare Pharmaceuticals Pvt. Ltd,, Chennai, India), for subgingival application has little reported data with clinical as well as antimicrobial efficacy. This study evaluated clinical and subgingival microbial changes on using indigenously developed PerioCol™CG as an adjunct to scaling and root planing (SRP) in the treatment of chronic periodontitis. Forty posterior first molar sites having probing pocket depth ≥ 5 mm were selected and divided into two groups, with 20 sites in each group, in a split-mouth design. Group A (test site) was treated with SRP and PerioCol(™)CG, while group B (control site) was treated with SRP alone. Subgingival microbial samples were collected at baseline and 1 month after the initial SRP, while probing depth (PD), clinical attachment level (CAL) and gingival index (GI) were recorded at baseline, after 1 month and after 3 months. Microbial detection of Porphyromonas gingivalis (P. gingivalis) and Tannerella forsythia (T. forsythia) was done by means of polymerase chain reaction (PCR). A significant improvement was observed in all clinical measures in sites treated with PerioCol(™)CG as compared to the control sites during the study period. Also, there was a statistically significant reduction in the proportion of occurrence of P. gingivalis and T. forsythia after intervention in test sites as compared to control sites. Our data suggest that SRP combined with subgingival administration of PerioCol™CG has a significantly better and prolonged effect compared to SRP alone on the PD, clinical attachment loss and elimination of periodontopathogens.