Periodontal disease encompasses gingivitis and periodontitis and is one of the most common chronic infections in the adult population. This study aimed to evaluate the influence of Spanish propolis extract (EEP) on the effect of the clinical and microbiological parameters as an adjuvant to scaling and root planning in patients undergoing supportive periodontal therapy (SPT). Forty chronic periodontitis patients were randomly assigned into two groups for the treatment. In the control group (n = 20), the sites were treated by scaling and root planing followed by gingival irrigation with physiological saline and in the test group (n = 20), the sites were treated by scaling and root planing followed by subgingival placement of EEP. At baseline (BL), bleeding on probing positive (BOP+) sites with probing pocket (PPD) ≥ 4 mm were defined as study sites. Plaque index, PPD, BOP, clinical attachment level (CAL), and subgingival plaque were evaluated at BL and 1 month later. The results showed a significant clinical improvement (p < 0.05) in the PPD, CAL and BOP+ comparing them with BL and one month after the periodontal treatment and a significant reduction (p < 0.05) for Tannerella forsythensis, Porphyromonas gingivalis, Prevotella intermedia and Treponema denticola in both groups. In addition, the improvement of clinical parameters was observed with subgingival use of EEP and also statistically significant differences between groups were observed (p < 0.05) such as reductions of BOP+ % and reduced counts of T. forsythensis and P. gingivalis, considered as the “key pathogens” for the periodontal diseases. Our results suggest prophylactic and therapeutic potential for EEP against periodontal diseases, improving clinical parameters, reducing gingival bleeding and decreasing bacterial counts of T. forsythensis and P. gingivalis. The subgingival use of EEP represents a promising modality as an adjuvant in periodontal therapy to avoid microbial resistance and other adverse effects.