ObjectiveDespite the clear drive from both research and clinical dentistry toward digital transformation, there are limitations to implementing intra-oral scanning (IOS) into daily dental practice. This study aimed to compare the precision of digital models obtained from two alternative indirect workflows to direct IOS.Material and methodsTwo indirect digital workflows were evaluated in this study. In the IOS group (direct), IOS directly obtained digital impressions of participants’ upper and lower dental arches, while in the Scan Impression (Scan Imp) group (indirect), a desktop scanner scanned silicone-based impressions of upper and lower whole arches that were taken with plastic trays. In the cone-beam computed tomography impression (CBCT Imp) group (indirect), a CBCT machine scanned the silicone-based impressions. Then, the precision of the entire arch and individual teeth for all digital impressions was virtually quantified. Following superimposition, differences between standard tessellation language (STL) files obtained from both—direct and indirect—methods were evaluated by color-mapping and measuring the surface distance between superimposed STL files. Furthermore, 18 linear measurements were taken from each digital model. ANOVA with repeated measures, Pearson coefficient, and intraclass correlation coefficient were used for intergroup comparisons.ResultsThe digital models obtained from the two indirect workflows differed from the IOS in some dental and intra-arch measurements but were considered clinically acceptable. Ranked against IOS, CBCT Imp models had greater precision, followed by Scan Imp.ConclusionDigital models obtained from two indirect, alternative workflows, desktop, and CBCT scanning of impression, have clinically acceptable accuracy and reliability of tooth size and intra-arch measurements, providing the use of proper methodologies.Clinical relevanceThere are some limitations to implementing IOS in daily clinical practice. However, several alternative digital model production techniques might provide an affordable solution. Although they may insignificantly differ in accuracy, all can be applied clinically.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00784-023-04996-2.