Here we report the synthesis, materials characterization, antimicrobial capacity, and cytocompatibility of novel antibiotic-containing scaffolds. Metronidazole (MET) or Ciprofloxacin/(CIP) was mixed with a polydioxanone (PDS)polymer solution at 5 and 25 wt% and processed into fibers. PDS fibers served as a control. Scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), tensile testing, and high-performance liquid chromatography (HPLC) were used to assess fiber morphology, chemical structure, mechanical properties, and drug release, respectively. Antimicrobial properties were evaluated against those of Porphyromonas gingivalis/Pg and Enterococcus faecalis/Ef. Cytotoxicity was assessed in human dental pulp stem cells (hDPSCs). Statistics were performed, and significance was set at the 5% level. SEM imaging revealed a submicron fiber diameter. FTIR confirmed antibiotic incorporation. The tensile values of hydrated 25 wt% CIP scaffold were significantly lower than those of all other groups. Analysis of HPLC data confirmed gradual, sustained drug release from the scaffolds over 48 hrs. CIP-containing scaffolds significantly (p < .00001) inhibited biofilm growth of both bacteria. Conversely, MET-containing scaffolds inhibited only Pg growth. Agar diffusion confirmed the antimicrobial properties against specific bacteria for the antibiotic-containing scaffolds. Only the 25 wt% CIP-containing scaffolds were cytotoxic. Collectively, this study suggests that polymer-based antibiotic-containing electrospun scaffolds could function as a biologically safe antimicrobial drug delivery system for regenerative endodontics.