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Breast cancer (BC) is the most commonly diagnosed non‐skin cancer in women. To achieve early and accurate diagnosis, three‐dimensional (3D) cone‐beam breast computed tomography (CBBCT) and digital breast tomosynthesis (DBT) modalities are used. Importantly, the comparison of reconstruction accuracy of both CBBCT and DBT has rarely been investigated, thus constituting a research gap. This study systematically investigated the performances of the CBBCT and DBT for different reconstruction algorithms using both BR3D breast phantom and breast images. We acquired clinical breast images and scanned the BR3D phantom for additional breast images. These acquired images were used to simulate projection data using predefined CBBCT and DBT geometries. The simulated projections were reconstructed using five different reconstruction algorithms. To evaluate the reconstruction accuracy, we calculated average image quality assessment (IQA) indices, including peak signal‐to‐noise ratio (PSNR), structural similarity index (SSIM), root mean square error (RMSE), and others, across different algorithms and modalities. The pooled PSNR, SSIM, and RMSE for DBT and CBBCT images are (31.6265 ± 0.8725), (0.9353 ± 0.0077), and (0.0270 ± 0.0025) and (29.7007 ± 0.9249), (0.9136 ± 0.0130), and (0.0342 ± 0.0040), which implies that the overall IQA indices of DBT are superior to CBBCT; therefore, DBT tends to reveal more BC detectability as the diagnosis outcome would largely depend on good quality images. The results show that DBT gives an improved result for all algorithms compared to CBBCT, although further experimental trials may be needed to establish the findings fully. The findings suggest that using DBT may enhance the accuracy of BC diagnosis compared to CBBCT due to its superior image quality in clinical practice, emphasizing the importance of selecting optimal reconstruction algorithms for improved diagnostic outcomes. [ABSTRACT FROM AUTHOR]