Objectives <p>Traditional complete denture (CD) design and fabrication techniques need several clinical and laboratory steps. To improve the qualities of denture base material and get rid of all the problems that come with the conventional fabrication process, novel production methods were approved. In the field of denture manufacture, new materials and computer-aided technology have been explored as potential solutions. So, this study aimed to investigate the effect of two different digital construction techniques of implant-assisted overdentures on peri-implant and posterior mandibular bone resorptions by CBCT.</p> Materials and methods <p>Twenty patients who received mandibular overdenture constructed by different construction techniques were classified equally and randomly into two groups (<i>n</i> = 10 per group): <b>Group M</b>: received milled mandibular overdenture opposed by maxillary complete denture. <b>Group P</b>: received 3D-printed mandibular overdenture opposed by maxillary complete denture. Peri-implant bone loss and posterior ridge resorption were assessed at baseline (T0), at 1 year(T1), and 3 years(T3) by superimposition of pre and post-treatment CBCT.The Shapiro-Wilk test was used to access data that was not normally distributed. Two distinct groups were compared using the Mann-Whitney test. The Wilcoxon signed-rank test was used to compare paired groups.</p> Results <p>Regarding vertical bone loss(VBL), Group P recorded higher VBL in comparison to Group M, where the mean was 0.57 ± 0.13, and 0.52 ± 0.12respectively, at T1 and 0.66 ± 0.11, 0.60 ± 0.12 at T3. There was a statistically significant difference at different times of evaluation within the groups where (<i>P</i> &lt; 0.001). Regarding posterior ridge resorption(PRR), Group P recorded higher PRR in comparison to Group M, where the mean was 381 ± 18.5, 333 ± 17.2 respectively at T1and 533 ± 24.9, 478.5 ± 12.3 at T3. There was a statistically significant difference at different times of evaluation within the groups where (<i>P</i> = 0.005).</p> Conclusion <p>Regarding the preservation of peri-implant alveolar bone and posterior ridge bone, milled implant-assisted complete overdentures may have more favorable clinical outcomes compared to 3D printed implant overdentures in the digitally constructed mandibular overdenture bases retained by two implants.</p> Clinical relevance <p>Both milled and 3D printed implant overdenture impression techniques can be used for the construction of CAD/CAM-implant retained overdenture base. However, in regarding the peri-implant alveolar bone and posterior ridge bone resorption, milled implant-assisted complete overdentures may have more favorable clinical outcomes compared to 3D printed implant overdentures retained by two implants.</p> Clinical trial registry number <p>(No.-NCT06720389) (03/12/2024).</p>