Abstract Aim: This study aimed to evaluate and compare the morphological and elemental characteristics of conventional Mineral Trioxide Aggregate (MTA) and Bacterial Cellulose-Reinforced MTA (BC-MTA) using Transmission Electron Microscopy (TEM) and Energy Dispersive X-ray Spectroscopy (EDX). Materials and Methods: Cylindrical molds (6 mm in diameter × 4 mm in height) were fabricated from plexiglass in accordance with ASTM E385 standards using CNC laser cutting. Two groups were evaluated: Group 1 comprised conventional MTA (MTA Plus™), and Group 2 comprised BC-MTA (Vedayukt India Pvt. Ltd.). The prepared samples were incubated under fully saturated conditions at 37°C for 24 hours. Following incubation, samples underwent morphological evaluation using TEM and elemental analysis using EDX. Statistical analysis was conducted using Student’s t-test, with results expressed as mean ± standard deviation (SD). A p-value < 0.0001 was considered highly statistically significant (α = 0.05). Results: TEM imaging revealed distinct structural differences between MTA and BC-MTA, with BC-MTA exhibiting a more aggregated nanoparticle morphology. EDX analysis demonstrated statistically significant differences in elemental composition between the two groups (p < 0.0001), confirming the influence of bacterial cellulose incorporation on the physiochemical properties of MTA. Conclusion: The incorporation of bacterial cellulose into MTA resulted in notable structural and elemental modifications, potentially enhancing its mechanical strength and bioactivity. These findings suggest that BC-MTA holds promise as an improved bioactive material in pediatric endodontic and restorative applications. Further clinical studies are warranted to assess its long-term efficacy and biocompatibility.