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The present study aimed to assess the in vitro antimicrobial effects of a novel biomaterial containing polylactic acid (PLA), nano-hydroxyapatite (nano-HAP) and Doxycycline (Doxy) obtained by electrospinning and designed for the non-surgical periodontal treatment. The antimicrobial activity of two samples (test sample, PLA-HAP-Doxy7: 5% PLA, nano-HAP, 7% Doxy and control sample, PLA-HAP: 5% PLA, nano-HAP) against two periodontal pathogens—Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis—was assessed using the Kirby–Bauer Disk Diffusion Susceptibility Test and compared with the effect of four antibiotics used as adjuvants in periodontal therapy: Amoxicillin, Ampicillin, Doxy and Metronidazole. The test sample (embedded with Doxy) showed higher inhibitory effects than commonly used antibiotics used in the treatment of periodontitis, while the control sample showed no inhibitory effects. Moreover, significant differences were observed between the inhibition zones of the two samples (p < 0.05). The Doxy-loaded PLA nanofibres had an antimicrobial effect against the periodontal pathogens. Based on these results, the novel biomaterial could be a promising candidate as adjuvant for the non-surgical local treatment in periodontitis.