Purpose: This study aimed to compare the marginal and internal fit of five-unit zirconia-based fixed dental prostheses (FDPs) fabricated using digital scans and conventional impressions. Materials and methods: Nine master models with three zirconia abutments were scanned with an intraoral scanner (test group), and nine conventional impressions (control group) of these same models were also made. The stone casts from these impressions were scanned with a laboratory extraoral scanner (D700, 3Shape, Copenhagen, Denmark). A total of 18 five-unit zirconia-based FDP frameworks (test group, n = 9; control group, n = 9) were manufactured. Marginal and internal fit (in μm) were evaluated using the replica method under micro-computed tomography. Analysis of variance (one-way ANOVA) and Kruskal–Wallis tests were used to compare continuous variables across two groups. A level of p < 0.05 was accepted as statistically significant. Results: The mean ± standard deviation of the marginal fit was 95.03 ± 12.74 μm in the test group and 106.02 ± 14.51 μm in the control group. The lowest marginal mean value was observed in the test group, with a statistically significant difference compared to the control group (F = 14.56, p < 0.05). The mean ± standard deviation of the internal fit was 103.61 ± 9.32 and 106.38 ± 7.64 μm, respectively, in the test and control groups, with no statistically significant difference (F = 1.56, p > 0.05). The mean values of both groups were clinically acceptable. Conclusions: The five-unit zirconia-based FDPs fabricated with digital scans showed better fit than those in the conventional impression group. Within the limitations of this study, these results are encouraging, and continued progress in the digital field should allow for more accurate long-span restorations.