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Aim: To evaluate the influence of different preparation tapers on the reduction in planktonic bacteria and biofilms of Enterococcus faecalis and Candida albicans in the apical third (4 mm) of the mesial roots of mandibular molars, correlating decontamination with canal shape. Methodology: After microtomography analysis for morphological standardization of the canals, 48 mandibular molar roots, each containing two canals (96 canals), were contaminated with E. faecalis and C. albicans and divided into four groups (n = 11) for canal instrumentation using ProDesign Logic 2 files with different tapers G (.03): # 25.03; G (.04): # 25.04; G (.05): # 25.05; and G (.06): # 25.06 and irrigation with 2.5% sodium hypochlorite. Four roots were examined under a scanning electron microscope (SEM) to qualitatively assess biofilm formation. Eight roots were used as the negative control group (samples were not contaminated). Bacteriological samples were taken exclusively from the apical third of the roots before and after chemical–mechanical preparation and bacterial counts were determined (CFU/mL). The final micro‐CT scan was used to quantify the volume variation and unprepared canal area in the apical third. Statistical analysis was performed using the Kruskal–Wallis, Student–Newman–Keuls and Wilcoxon tests for analysis of microbiological data. anova and the Tukey or Games–Howell test were used for analysis of micro‐CT data and Spearman's test for correlations (α = 5%). Results: All groups showed a significant reduction in bacteria (p <.05), with no statistically significant difference between groups. There was no significant difference in per cent volume increase between groups. The unprepared area (Δ%) was affected by the file used (p =.026) and was significantly lower for G (.06) compared to G (.03). There was no statistically significant correlation among bacterial reduction, volume and unprepared area (p >.05). Conclusion: The different preparation tapers influenced root canal shaping in the apical third but did not improve decontamination in this region. [ABSTRACT FROM AUTHOR]